0.013876 0.008011 0.000000 0.000000 0.016023 0.000000 0.000000 0.000000 0.011230 0.00000 0.00000 0.00000 6 6 2.3103 1.0201 1.5888 0.8651 20.8439 10.2075 0.5687 51.6512 7 7 12.2220 3.1346 2.0141 1.1672 0.0057 9.8933 28.9975 0.5826 8 8 3.0487 2.2870 1.5464 0.8671 13.2771 5.7011 0.3239 32.9089 16 16 6.9054 5.2035 1.4379 1.5863 1.4679 22.2151 0.2536 56.1720 0000-0002-0307-0907 Plewka, J. 0009-0003-8971-8587 Golebiowska-Mendroch, K. 0009-0006-2247-3302 Slota, A. 0000-0002-4826-6380 Magiera-Mularz, K. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90 90 120 72.066 72.066 89.048 C41 H41 N7 O4 695.809 (3~{R})-1-[[7-(iminomethyl)-2-[2-methyl-3-[2-methyl-3-[[3-[[(3~{R})-3-oxidanylpyrrolidin-1-yl]methyl]-1,7-naphthyridin-8-yl]amino]phenyl]phenyl]-1,3-benzoxazol-5-yl]methyl]pyrrolidine-3-carboxylic acid non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking Y 1 N C Y 2 N C Y 3 N C Y 4 N C N 5 N C N 6 N C N 7 N C N 8 R C N 9 N C Y 10 N C Y 11 N C Y 12 N C Y 13 N C N 14 N C N 15 N N N 16 N C Y 17 N C Y 18 N C Y 19 N C Y 20 N N Y 21 N C Y 22 N C Y 23 N C Y 24 N C Y 25 N C Y 26 N C Y 27 N C N 28 N N Y 29 N C Y 30 N N Y 31 N C Y 32 N C Y 33 N N N 34 N N N 35 N O Y 36 N C Y 37 N C Y 38 N C N 39 N C Y 40 N O Y 41 N C Y 42 N C N 43 N C N 44 N N N 45 N C N 46 R C N 47 N C N 48 N C N 49 N C N 50 N O N 51 N O Y 52 N C N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N N N 95 S C N 96 N C N 97 N O N 98 N C N 99 N O N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N N N 108 S C N 109 N C N 110 N O N 111 N C N 112 N C N 113 N C N 114 N N N 115 N C N 116 N N N 117 N N N 118 N O N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N N N 135 S C N 136 N C N 137 N O N 138 N C N 139 N C N 140 N O N 141 N N N 142 N O N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N N N 152 S C N 153 N C N 154 N O N 155 N C N 156 N C N 157 N O N 158 N O N 159 N O N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N N N 168 R C N 169 N C N 170 N O N 171 N C N 172 N S N 173 N O N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N N N 182 S C N 183 N C N 184 N O N 185 N C N 186 N C N 187 N C N 188 N O N 189 N N N 190 N O N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N N N 202 S C N 203 N C N 204 N O N 205 N C N 206 N C N 207 N C N 208 N O N 209 N O N 210 N O N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N N N 221 N C N 222 N C N 223 N O N 224 N O N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N N N 231 S C N 232 N C N 233 N O N 234 N C Y 235 N C Y 236 N N Y 237 N C Y 238 N C Y 239 N N N 240 N O N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N O N 252 N H N 253 N H N 254 N N N 255 S C N 256 N C N 257 N O N 258 S C N 259 N C N 260 N C N 261 N C N 262 N O N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N N N 277 S C N 278 N C N 279 N O N 280 N C N 281 N C N 282 N C N 283 N C N 284 N O N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N H N 296 N H N 297 N H N 298 N N N 299 S C N 300 N C N 301 N O N 302 N C N 303 N C N 304 N C N 305 N C N 306 N N N 307 N O N 308 N H N 309 N H N 310 N H N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N H N 322 N H N 323 N N N 324 S C N 325 N C N 326 N O N 327 N C N 328 N C N 329 N S N 330 N C N 331 N O N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N H N 341 N H N 342 N H N 343 N N N 344 S C N 345 N C N 346 N O N 347 N C Y 348 N C Y 349 N C Y 350 N C Y 351 N C Y 352 N C Y 353 N C N 354 N O N 355 N H N 356 N H N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N N N 367 S C N 368 N C N 369 N O N 370 N C N 371 N C N 372 N C N 373 N O N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N N N 384 S C N 385 N C N 386 N O N 387 N C N 388 N O N 389 N O N 390 N H N 391 N H N 392 N H N 393 N H N 394 N H N 395 N H N 396 N H N 397 N N N 398 S C N 399 N C N 400 N O N 401 R C N 402 N O N 403 N C N 404 N O N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N H N 414 N N N 415 S C N 416 N C N 417 N O N 418 N C Y 419 N C Y 420 N C Y 421 N C Y 422 N N Y 423 N C Y 424 N C Y 425 N C Y 426 N C Y 427 N C N 428 N O N 429 N H N 430 N H N 431 N H N 432 N H N 433 N H N 434 N H N 435 N H N 436 N H N 437 N H N 438 N H N 439 N H N 440 N H N 441 N N N 442 S C N 443 N C N 444 N O N 445 N C Y 446 N C Y 447 N C Y 448 N C Y 449 N C Y 450 N C Y 451 N C N 452 N O N 453 N O N 454 N H N 455 N H N 456 N H N 457 N H N 458 N H N 459 N H N 460 N H N 461 N H N 462 N H N 463 N H N 464 N H N 465 N N N 466 S C N 467 N C N 468 N O N 469 N C N 470 N C N 471 N C N 472 N O N 473 N H N 474 N H N 475 N H N 476 N H N 477 N H N 478 N H N 479 N H N 480 N H N 481 N H N 482 N H N 483 N H N 1 N sing N 2 N sing N 3 N sing N 4 N doub N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing Y 11 N doub Y 12 N sing Y 13 N sing N 14 N sing Y 15 N doub N 16 N doub Y 17 N doub Y 18 N sing Y 19 N sing Y 20 N sing Y 21 N sing Y 22 N doub N 23 N sing Y 24 N doub Y 25 N sing Y 26 N sing N 27 N sing Y 28 N doub Y 29 N doub Y 30 N sing N 31 N sing Y 32 N doub Y 33 N sing Y 34 N sing Y 35 N doub N 36 N sing Y 37 N doub Y 38 N sing N 39 N sing N 40 N sing Y 41 N doub Y 42 N sing Y 43 N sing Y 44 N doub Y 45 N sing Y 46 N doub Y 47 N sing Y 48 N doub Y 49 N sing Y 50 N sing Y 51 N doub N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N doub N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N doub N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N doub N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N doub N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N doub N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N doub N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N doub N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N doub N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N doub N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N doub N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N doub N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N doub N 236 N sing N 237 N sing N 238 N sing N 239 N sing Y 240 N sing Y 241 N doub Y 242 N doub N 243 N sing Y 244 N sing N 245 N sing Y 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N doub N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N doub N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N doub N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N doub N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N doub N 344 N sing N 345 N sing N 346 N sing N 347 N sing Y 348 N doub Y 349 N sing Y 350 N sing N 351 N sing Y 352 N doub N 353 N sing Y 354 N doub N 355 N sing Y 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N doub N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N doub N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing N 395 N sing N 396 N doub N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N sing N 410 N sing N 411 N sing N 412 N doub N 413 N sing N 414 N sing N 415 N sing N 416 N sing Y 417 N doub Y 418 N sing Y 419 N sing N 420 N sing Y 421 N doub Y 422 N sing Y 423 N sing N 424 N sing Y 425 N sing Y 426 N doub N 427 N sing Y 428 N doub N 429 N sing Y 430 N sing N 431 N sing N 432 N sing N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N sing N 440 N doub N 441 N sing N 442 N sing N 443 N sing N 444 N sing Y 445 N doub Y 446 N sing Y 447 N sing N 448 N sing Y 449 N doub N 450 N sing Y 451 N doub N 452 N sing Y 453 N sing N 454 N sing N 455 N sing N 456 N sing N 457 N sing N 458 N sing N 459 N sing N 460 N sing N 461 N sing N 462 N sing N 463 N sing N 464 N doub N 465 N sing N 466 N sing N 467 N sing N 468 N sing N 469 N sing N 470 N sing N 471 N sing N 472 N sing N 473 N sing N 474 N sing N 475 N sing US Acs Med.Chem.Lett. 1948-5875 16 1359 1364 10.1021/acsmedchemlett.5c00245 40666457 Characterization of Clinically Evaluated Small-Molecule Inhibitors of PD-L1 for Immunotherapy. 2025 10.2210/pdb9i0w/pdb pdb_00009i0w 100 1 N PIXEL 2024-11-15 DECTRIS PILATUS 6M SINGLE WAVELENGTH M x-ray 1 0.968 1.0 MASSIF-1 ESRF 0.968 SYNCHROTRON ESRF BEAMLINE MASSIF-1 14954.085 Programmed cell death 1 ligand 1 2 man polymer 695.809 (3~{R})-1-[[7-(iminomethyl)-2-[2-methyl-3-[2-methyl-3-[[3-[[(3~{R})-3-oxidanylpyrrolidin-1-yl]methyl]-1,7-naphthyridin-8-yl]amino]phenyl]phenyl]-1,3-benzoxazol-5-yl]methyl]pyrrolidine-3-carboxylic acid 1 syn non-polymer 18.015 water 3 nat water PD-L1,PDCD1 ligand 1,Programmed death ligand 1,hPD-L1,B7 homolog 1,B7-H1 no no MGSAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSL GNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHHHHHH MGSAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSL GNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHHHHHH A,B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human sample 1 131 CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 9606 Homo sapiens 562 Escherichia coli Biological sequence 1 2.23 44.89 VAPOR DIFFUSION, HANGING DROP 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350 293 citation repository Initial release Database references 1 0 2025-06-18 1 1 2025-07-30 _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_PubMed _citation.title Poland Polish National Science Centre 2021/43/B/NZ7/03170 k.magiera@uj.edu.pl 0000-0002-4826-6380 Katarzyna Magiera-Mularz principal investigator/group leader N PDBE N PDBE 2025-01-15 REL REL A1IZP A1IZP SUBJECT OF INVESTIGATION A1IZP (3~{R})-1-[[7-(iminomethyl)-2-[2-methyl-3-[2-methyl-3-[[3-[[(3~{R})-3-oxidanylpyrrolidin-1-yl]methyl]-1,7-naphthyridin-8-yl]amino]phenyl]phenyl]-1,3-benzoxazol-5-yl]methyl]pyrrolidine-3-carboxylic acid HOH water Y Y 5J89 PDB experimental model A CYS 40 Disulfide bridge SG A CYS 26 A CYS 114 SG A CYS 100 1_555 1_555 None B CYS 40 Disulfide bridge SG B CYS 26 B CYS 114 SG B CYS 100 1_555 1_555 None 00Z 1 2 A1IZP A1IZP 201 B HOH 2 3 HOH HOH 201 A HOH 3 3 HOH HOH 301 B HOH 1 3 HOH HOH 302 B n 1 15 A n 2 16 A n 3 17 A ALA 18 n 4 ALA 18 A PHE 19 n 5 PHE 19 A THR 20 n 6 THR 20 A VAL 21 n 7 VAL 21 A THR 22 n 8 THR 22 A VAL 23 n 9 VAL 23 A PRO 24 n 10 PRO 24 A LYS 25 n 11 LYS 25 A ASP 26 n 12 ASP 26 A LEU 27 n 13 LEU 27 A TYR 28 n 14 TYR 28 A VAL 29 n 15 VAL 29 A VAL 30 n 16 VAL 30 A GLU 31 n 17 GLU 31 A TYR 32 n 18 TYR 32 A GLY 33 n 19 GLY 33 A SER 34 n 20 SER 34 A ASN 35 n 21 ASN 35 A MET 36 n 22 MET 36 A THR 37 n 23 THR 37 A ILE 38 n 24 ILE 38 A GLU 39 n 25 GLU 39 A CYS 40 n 26 CYS 40 A LYS 41 n 27 LYS 41 A PHE 42 n 28 PHE 42 A PRO 43 n 29 PRO 43 A VAL 44 n 30 VAL 44 A GLU 45 n 31 GLU 45 A LYS 46 n 32 LYS 46 A GLN 47 n 33 GLN 47 A LEU 48 n 34 LEU 48 A ASP 49 n 35 ASP 49 A LEU 50 n 36 LEU 50 A ALA 51 n 37 ALA 51 A ALA 52 n 38 ALA 52 A LEU 53 n 39 LEU 53 A ILE 54 n 40 ILE 54 A VAL 55 n 41 VAL 55 A TYR 56 n 42 TYR 56 A TRP 57 n 43 TRP 57 A GLU 58 n 44 GLU 58 A MET 59 n 45 MET 59 A GLU 60 n 46 GLU 60 A ASP 61 n 47 ASP 61 A LYS 62 n 48 LYS 62 A ASN 63 n 49 ASN 63 A ILE 64 n 50 ILE 64 A ILE 65 n 51 ILE 65 A GLN 66 n 52 GLN 66 A PHE 67 n 53 PHE 67 A VAL 68 n 54 VAL 68 A HIS 69 n 55 HIS 69 A GLY 70 n 56 GLY 70 A GLU 71 n 57 GLU 71 A GLU 72 n 58 GLU 72 A ASP 73 n 59 ASP 73 A LEU 74 n 60 LEU 74 A LYS 75 n 61 LYS 75 A VAL 76 n 62 VAL 76 A GLN 77 n 63 GLN 77 A HIS 78 n 64 HIS 78 A SER 79 n 65 SER 79 A SER 80 n 66 SER 80 A TYR 81 n 67 TYR 81 A ARG 82 n 68 ARG 82 A GLN 83 n 69 GLN 83 A ARG 84 n 70 ARG 84 A ALA 85 n 71 ALA 85 A ARG 86 n 72 ARG 86 A LEU 87 n 73 LEU 87 A LEU 88 n 74 LEU 88 A LYS 89 n 75 LYS 89 A ASP 90 n 76 ASP 90 A GLN 91 n 77 GLN 91 A LEU 92 n 78 LEU 92 A SER 93 n 79 SER 93 A LEU 94 n 80 LEU 94 A GLY 95 n 81 GLY 95 A ASN 96 n 82 ASN 96 A ALA 97 n 83 ALA 97 A ALA 98 n 84 ALA 98 A LEU 99 n 85 LEU 99 A GLN 100 n 86 GLN 100 A ILE 101 n 87 ILE 101 A THR 102 n 88 THR 102 A ASP 103 n 89 ASP 103 A VAL 104 n 90 VAL 104 A LYS 105 n 91 LYS 105 A LEU 106 n 92 LEU 106 A GLN 107 n 93 GLN 107 A ASP 108 n 94 ASP 108 A ALA 109 n 95 ALA 109 A GLY 110 n 96 GLY 110 A VAL 111 n 97 VAL 111 A TYR 112 n 98 TYR 112 A ARG 113 n 99 ARG 113 A CYS 114 n 100 CYS 114 A MET 115 n 101 MET 115 A ILE 116 n 102 ILE 116 A SER 117 n 103 SER 117 A TYR 118 n 104 TYR 118 A GLY 119 n 105 GLY 119 A GLY 120 n 106 GLY 120 A ALA 121 n 107 ALA 121 A ASP 122 n 108 ASP 122 A TYR 123 n 109 TYR 123 A LYS 124 n 110 LYS 124 A ARG 125 n 111 ARG 125 A ILE 126 n 112 ILE 126 A THR 127 n 113 THR 127 A VAL 128 n 114 VAL 128 A LYS 129 n 115 LYS 129 A VAL 130 n 116 VAL 130 A ASN 131 n 117 ASN 131 A ALA 132 n 118 ALA 132 A n 119 133 A n 120 134 A n 121 135 A n 122 136 A n 123 137 A n 124 138 A n 125 139 A n 126 140 A n 127 141 A n 128 142 A n 129 143 A n 130 144 A n 131 145 A n 1 15 B n 2 16 B n 3 17 B ALA 18 n 4 ALA 18 B PHE 19 n 5 PHE 19 B THR 20 n 6 THR 20 B VAL 21 n 7 VAL 21 B THR 22 n 8 THR 22 B VAL 23 n 9 VAL 23 B PRO 24 n 10 PRO 24 B LYS 25 n 11 LYS 25 B ASP 26 n 12 ASP 26 B LEU 27 n 13 LEU 27 B TYR 28 n 14 TYR 28 B VAL 29 n 15 VAL 29 B VAL 30 n 16 VAL 30 B GLU 31 n 17 GLU 31 B TYR 32 n 18 TYR 32 B GLY 33 n 19 GLY 33 B SER 34 n 20 SER 34 B ASN 35 n 21 ASN 35 B MET 36 n 22 MET 36 B THR 37 n 23 THR 37 B ILE 38 n 24 ILE 38 B GLU 39 n 25 GLU 39 B CYS 40 n 26 CYS 40 B LYS 41 n 27 LYS 41 B PHE 42 n 28 PHE 42 B PRO 43 n 29 PRO 43 B VAL 44 n 30 VAL 44 B GLU 45 n 31 GLU 45 B LYS 46 n 32 LYS 46 B GLN 47 n 33 GLN 47 B LEU 48 n 34 LEU 48 B ASP 49 n 35 ASP 49 B LEU 50 n 36 LEU 50 B ALA 51 n 37 ALA 51 B ALA 52 n 38 ALA 52 B LEU 53 n 39 LEU 53 B ILE 54 n 40 ILE 54 B VAL 55 n 41 VAL 55 B TYR 56 n 42 TYR 56 B TRP 57 n 43 TRP 57 B GLU 58 n 44 GLU 58 B MET 59 n 45 MET 59 B GLU 60 n 46 GLU 60 B ASP 61 n 47 ASP 61 B LYS 62 n 48 LYS 62 B ASN 63 n 49 ASN 63 B ILE 64 n 50 ILE 64 B ILE 65 n 51 ILE 65 B GLN 66 n 52 GLN 66 B PHE 67 n 53 PHE 67 B VAL 68 n 54 VAL 68 B HIS 69 n 55 HIS 69 B GLY 70 n 56 GLY 70 B GLU 71 n 57 GLU 71 B GLU 72 n 58 GLU 72 B ASP 73 n 59 ASP 73 B LEU 74 n 60 LEU 74 B LYS 75 n 61 LYS 75 B VAL 76 n 62 VAL 76 B GLN 77 n 63 GLN 77 B HIS 78 n 64 HIS 78 B SER 79 n 65 SER 79 B SER 80 n 66 SER 80 B TYR 81 n 67 TYR 81 B ARG 82 n 68 ARG 82 B GLN 83 n 69 GLN 83 B ARG 84 n 70 ARG 84 B ALA 85 n 71 ALA 85 B ARG 86 n 72 ARG 86 B LEU 87 n 73 LEU 87 B LEU 88 n 74 LEU 88 B LYS 89 n 75 LYS 89 B ASP 90 n 76 ASP 90 B GLN 91 n 77 GLN 91 B LEU 92 n 78 LEU 92 B SER 93 n 79 SER 93 B LEU 94 n 80 LEU 94 B GLY 95 n 81 GLY 95 B ASN 96 n 82 ASN 96 B ALA 97 n 83 ALA 97 B ALA 98 n 84 ALA 98 B LEU 99 n 85 LEU 99 B GLN 100 n 86 GLN 100 B ILE 101 n 87 ILE 101 B THR 102 n 88 THR 102 B ASP 103 n 89 ASP 103 B VAL 104 n 90 VAL 104 B LYS 105 n 91 LYS 105 B LEU 106 n 92 LEU 106 B GLN 107 n 93 GLN 107 B ASP 108 n 94 ASP 108 B ALA 109 n 95 ALA 109 B GLY 110 n 96 GLY 110 B VAL 111 n 97 VAL 111 B TYR 112 n 98 TYR 112 B ARG 113 n 99 ARG 113 B CYS 114 n 100 CYS 114 B MET 115 n 101 MET 115 B ILE 116 n 102 ILE 116 B SER 117 n 103 SER 117 B TYR 118 n 104 TYR 118 B GLY 119 n 105 GLY 119 B GLY 120 n 106 GLY 120 B ALA 121 n 107 ALA 121 B ASP 122 n 108 ASP 122 B TYR 123 n 109 TYR 123 B LYS 124 n 110 LYS 124 B ARG 125 n 111 ARG 125 B ILE 126 n 112 ILE 126 B THR 127 n 113 THR 127 B VAL 128 n 114 VAL 128 B LYS 129 n 115 LYS 129 B VAL 130 n 116 VAL 130 B ASN 131 n 117 ASN 131 B ALA 132 n 118 ALA 132 B PRO 133 n 119 PRO 133 B n 120 134 B n 121 135 B n 122 136 B n 123 137 B n 124 138 B n 125 139 B n 126 140 B n 127 141 B n 128 142 B n 129 143 B n 130 144 B n 131 145 B author_defined_assembly 2 dimeric none 1470 -1 11530 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N TYR 28 A N TYR 14 A O LYS 129 A O LYS 115 A O ILE 126 A O ILE 112 A N TYR 112 A N TYR 98 A O MET 115 A O MET 101 A N TYR 56 A N TYR 42 A N MET 59 A N MET 45 A O LYS 62 A O LYS 48 A N VAL 68 A N VAL 54 A O GLU 71 A O GLU 57 A N MET 36 A N MET 22 A O ILE 101 A O ILE 87 A O GLN 100 A O GLN 86 A N ARG 86 A N ARG 72 B N VAL 30 B N VAL 16 B O LYS 129 B O LYS 115 B O ILE 126 B O ILE 112 B N TYR 112 B N TYR 98 B O MET 115 B O MET 101 B N TYR 56 B N TYR 42 B N MET 59 B N MET 45 B O LYS 62 B O LYS 48 B N VAL 68 B N VAL 54 B O GLU 71 B O GLU 57 B N MET 36 B N MET 22 B O ILE 101 B O ILE 87 B O GLN 100 B O GLN 86 B N ARG 86 B N ARG 72 1 A CG LYS 46 A CG LYS 32 1 Y 1 A CD LYS 46 A CD LYS 32 1 Y 1 A CE LYS 46 A CE LYS 32 1 Y 1 A NZ LYS 46 A NZ LYS 32 1 Y 1 A CG GLN 47 A CG GLN 33 1 Y 1 A CD GLN 47 A CD GLN 33 1 Y 1 A OE1 GLN 47 A OE1 GLN 33 1 Y 1 A NE2 GLN 47 A NE2 GLN 33 1 Y 1 A CG GLU 71 A CG GLU 57 1 Y 1 A CD GLU 71 A CD GLU 57 1 Y 1 A OE1 GLU 71 A OE1 GLU 57 1 Y 1 A OE2 GLU 71 A OE2 GLU 57 1 Y 1 B CG LYS 75 B CG LYS 61 1 Y 1 B CD LYS 75 B CD LYS 61 1 Y 1 B CE LYS 75 B CE LYS 61 1 Y 1 B NZ LYS 75 B NZ LYS 61 1 Y 1 B CG1 VAL 76 B CG1 VAL 62 1 Y 1 B CG2 VAL 76 B CG2 VAL 62 1 Y 1 B CG GLN 77 B CG GLN 63 1 Y 1 B CD GLN 77 B CD GLN 63 1 Y 1 B OE1 GLN 77 B OE1 GLN 63 1 Y 1 B NE2 GLN 77 B NE2 GLN 63 1 Y 1 B OG SER 80 B OG SER 66 1 Y 1 B CG ASP 90 B CG ASP 76 1 Y 1 B OD1 ASP 90 B OD1 ASP 76 1 Y 1 B OD2 ASP 90 B OD2 ASP 76 1 Y 1 A MET 15 A MET 1 1 Y 1 A GLY 16 A GLY 2 1 Y 1 A SER 17 A SER 3 1 Y 1 A PRO 133 A PRO 119 1 Y 1 A TYR 134 A TYR 120 1 Y 1 A ALA 135 A ALA 121 1 Y 1 A ALA 136 A ALA 122 1 Y 1 A ALA 137 A ALA 123 1 Y 1 A LEU 138 A LEU 124 1 Y 1 A GLU 139 A GLU 125 1 Y 1 A HIS 140 A HIS 126 1 Y 1 A HIS 141 A HIS 127 1 Y 1 A HIS 142 A HIS 128 1 Y 1 A HIS 143 A HIS 129 1 Y 1 A HIS 144 A HIS 130 1 Y 1 A HIS 145 A HIS 131 1 Y 1 B MET 15 B MET 1 1 Y 1 B GLY 16 B GLY 2 1 Y 1 B SER 17 B SER 3 1 Y 1 B TYR 134 B TYR 120 1 Y 1 B ALA 135 B ALA 121 1 Y 1 B ALA 136 B ALA 122 1 Y 1 B ALA 137 B ALA 123 1 Y 1 B LEU 138 B LEU 124 1 Y 1 B GLU 139 B GLU 125 1 Y 1 B HIS 140 B HIS 126 1 Y 1 B HIS 141 B HIS 127 1 Y 1 B HIS 142 B HIS 128 1 Y 1 B HIS 143 B HIS 129 1 Y 1 B HIS 144 B HIS 130 1 Y 1 B HIS 145 B HIS 131 1 Y 1 B B GLN HIS 77 78 -145.96 1 A ARG 86 0.091 SIDE CHAIN 1 12.78 1.60 100.20 112.98 A A A CG SD CE MET MET MET 59 59 59 N 1 -10.55 1.70 111.00 100.45 A A A CB CG CD1 LEU LEU LEU 74 74 74 N 1 12.62 1.70 111.00 123.62 A A A CB CG CD2 LEU LEU LEU 74 74 74 N 1 13.18 2.00 110.40 123.58 A A A CB CA C LYS LYS LYS 75 75 75 N 1 12.27 1.70 111.00 123.27 A A A CB CG CD1 LEU LEU LEU 88 88 88 N 1 11.44 1.70 111.00 122.44 A A A CB CG CD1 LEU LEU LEU 94 94 94 N 1 10.82 1.40 123.60 134.42 A A A CD NE CZ ARG ARG ARG 113 113 113 N 1 4.37 0.50 120.30 124.67 A A A NE CZ NH2 ARG ARG ARG 113 113 113 N 1 -12.22 1.80 110.60 98.38 B B B N CA CB GLN GLN GLN 66 66 66 N 1 -4.95 0.50 120.30 115.35 B B B NE CZ NH2 ARG ARG ARG 82 82 82 N 1 10.05 1.40 123.60 133.65 B B B CD NE CZ ARG ARG ARG 113 113 113 N 1 -4.29 0.50 120.30 116.01 B B B NE CZ NH2 ARG ARG ARG 125 125 125 N 1 -13.54 2.00 110.40 96.86 B B B CB CA C ASN ASN ASN 131 131 131 N 1 A PHE 19 -29.27 111.56 1 A LYS 46 -137.86 -159.20 1 A GLU 60 39.52 51.96 1 A ILE 64 -105.46 -60.76 1 A ASP 103 60.94 68.06 1 A TYR 118 -158.19 85.50 1 B SER 34 -66.99 -168.49 1 B LYS 46 64.13 -117.15 1 B ASP 61 81.33 -5.10 1 B LEU 74 -98.24 49.24 1 B ARG 82 85.21 -36.23 1 B ASP 103 61.31 71.58 1 B TYR 118 -157.15 84.61 50.110 -1.080 -0.540 0.000 -1.080 0.000 3.504 0.952 0.916 Hydrogens have not been used 0.2995 0.2338 0.237 2.100 36.246 750 14514 15264 4.914 94.890 10.518 0.248 1 FREE R-VALUE MOLECULAR REPLACEMENT 0.263 0.234 0.800 0.800 1.200 MASK BULK SOLVENT 2.100 36.246 3 1880 52 0 1825 0.012 0.012 1917 2.720 1.832 2603 8.421 5.000 229 28.194 5.000 16 17.159 10.000 329 14.558 10.000 84 0.179 0.200 292 0.013 0.020 1444 0.196 0.200 685 0.293 0.200 1241 0.145 0.200 57 0.272 0.200 29 0.173 0.200 1 7.556 4.768 922 10.822 8.556 1149 9.567 5.080 995 13.292 9.087 1454 16.937 52.244 2670 0.139 0.050 3036 1 A 1 X-RAY DIFFRACTION Local ncs 0.13927 0.05007 2 B 1 X-RAY DIFFRACTION Local ncs 0.13927 0.05007 0.436 0.414 0.414 2.155 50 1111 1161 0.838 0.858 20 100.0000 0.411 0.304 0.388 0.383 2.213 51 1076 1127 0.914 0.866 20 100.0000 0.383 0.481 0.380 0.385 2.277 41 930 1105 0.793 0.867 20 87.8733 0.373 0.379 0.350 0.351 2.347 57 1041 1098 0.878 0.889 20 100.0000 0.341 0.285 0.315 0.314 2.424 35 1001 1036 0.945 0.907 20 100.0000 0.297 0.364 0.321 0.323 2.508 50 961 1011 0.882 0.913 20 100.0000 0.304 0.389 0.294 0.299 2.603 51 940 991 0.901 0.925 20 100.0000 0.273 0.345 0.272 0.277 2.708 43 612 919 0.912 0.942 20 71.2731 0.250 0.270 0.241 0.243 2.828 47 863 911 0.956 0.956 20 99.8902 0.218 0.349 0.226 0.233 2.965 50 819 871 0.935 0.964 20 99.7704 0.201 0.336 0.218 0.223 3.124 42 789 832 0.932 0.966 20 99.8798 0.192 0.317 0.216 0.220 3.312 40 747 789 0.945 0.965 20 99.7465 0.196 0.365 0.225 0.235 3.539 41 546 726 0.917 0.964 20 80.8540 0.204 0.220 0.192 0.194 3.819 31 520 707 0.966 0.975 20 77.9349 0.177 0.221 0.169 0.172 4.179 24 499 640 0.981 0.983 20 81.7188 0.166 0.158 0.129 0.130 4.665 21 561 583 0.986 0.990 20 99.8285 0.130 0.221 0.163 0.165 5.372 19 501 520 0.974 0.983 20 100.0000 0.168 0.290 0.213 0.218 6.543 34 432 466 0.941 0.968 20 100.0000 0.220 0.366 0.261 0.265 9.106 14 344 359 0.925 0.951 20 99.7215 0.270 0.361 0.259 0.262 36.246 9 221 231 0.876 0.955 20 99.5671 0.294 2.10 62.41 9I0W 15292 0.995 0.181 0.118 0.218 1.03 1 6.0 5.9 94.9 0.046 8.91 62.41 19.3 249 0.997 0.031 0.055 0.61 5.1 98.6 1.644 2.10 2.16 1.1 1312 0.146 1.063 1.966 0.90 6.3 100.0 refinement REFMAC 5.8.0430 (refmacat 0.4.88) refinement REFMAC 5.8.0430 (refmacat 0.4.88) data scaling Aimless data reduction XDS data scaling Aimless phasing PHASER N Structure of human PD-L1 in complex with clinically evaluated inhibitor 1 N N 1 N N 2 N N 3 N N 3 N N A ASP 49 A ASP 35 HELX_P A ALA 52 A ALA 38 5 AA1 4 A LEU 74 A LEU 60 HELX_P A GLN 77 A GLN 63 5 AA2 4 A HIS 78 A HIS 64 HELX_P A ARG 82 A ARG 68 5 AA3 5 A LEU 88 A LEU 74 HELX_P A SER 93 A SER 79 1 AA4 6 B ASP 49 B ASP 35 HELX_P B ALA 52 B ALA 38 5 AA5 4 B LEU 88 B LEU 74 HELX_P B SER 93 B SER 79 1 AA6 6 disulf 2.007 A CYS 40 A SG CYS 26 1_555 A CYS 114 A SG CYS 100 1_555 disulf 2.082 B CYS 40 B SG CYS 26 1_555 B CYS 114 B SG CYS 100 1_555 IMMUNE SYSTEM small-molecule inhibitor, PD-1 pathway, Programmed death-ligand 1, IMMUNE SYSTEM A B A ALA 18 A ALA 4 A ASN 131 A ASN 117 B ALA 18 B ALA 4 B ASN 131 B ASN 117 Local NCS retraints between domains: 1 2 PD1L1_HUMAN UNP 1 18 Q9NZQ7 AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNA ALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPY 18 134 9I0W 18 134 Q9NZQ7 A 1 4 120 18 134 9I0W 18 134 Q9NZQ7 B 1 4 120 1 initiating methionine MET 15 9I0W A Q9NZQ7 UNP 1 1 expression tag GLY 16 9I0W A Q9NZQ7 UNP 2 1 expression tag SER 17 9I0W A Q9NZQ7 UNP 3 1 expression tag ALA 135 9I0W A Q9NZQ7 UNP 121 1 expression tag ALA 136 9I0W A Q9NZQ7 UNP 122 1 expression tag ALA 137 9I0W A Q9NZQ7 UNP 123 1 expression tag LEU 138 9I0W A Q9NZQ7 UNP 124 1 expression tag GLU 139 9I0W A Q9NZQ7 UNP 125 1 expression tag HIS 140 9I0W A Q9NZQ7 UNP 126 1 expression tag HIS 141 9I0W A Q9NZQ7 UNP 127 1 expression tag HIS 142 9I0W A Q9NZQ7 UNP 128 1 expression tag HIS 143 9I0W A Q9NZQ7 UNP 129 1 expression tag HIS 144 9I0W A Q9NZQ7 UNP 130 1 expression tag HIS 145 9I0W A Q9NZQ7 UNP 131 2 initiating methionine MET 15 9I0W B Q9NZQ7 UNP 1 2 expression tag GLY 16 9I0W B Q9NZQ7 UNP 2 2 expression tag SER 17 9I0W B Q9NZQ7 UNP 3 2 expression tag ALA 135 9I0W B Q9NZQ7 UNP 121 2 expression tag ALA 136 9I0W B Q9NZQ7 UNP 122 2 expression tag ALA 137 9I0W B Q9NZQ7 UNP 123 2 expression tag LEU 138 9I0W B Q9NZQ7 UNP 124 2 expression tag GLU 139 9I0W B Q9NZQ7 UNP 125 2 expression tag HIS 140 9I0W B Q9NZQ7 UNP 126 2 expression tag HIS 141 9I0W B Q9NZQ7 UNP 127 2 expression tag HIS 142 9I0W B Q9NZQ7 UNP 128 2 expression tag HIS 143 9I0W B Q9NZQ7 UNP 129 2 expression tag HIS 144 9I0W B Q9NZQ7 UNP 130 2 expression tag HIS 145 9I0W B Q9NZQ7 UNP 131 6 3 6 3 parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A LEU 27 A LEU 13 A GLU 31 A GLU 17 A ALA 121 A ALA 107 A ASN 131 A ASN 117 A GLY 110 A GLY 96 A SER 117 A SER 103 A ILE 54 A ILE 40 A MET 59 A MET 45 A LYS 62 A LYS 48 A VAL 68 A VAL 54 A GLU 71 A GLU 57 A GLU 72 A GLU 58 A ASN 35 A ASN 21 A LYS 41 A LYS 27 A ASN 96 A ASN 82 A THR 102 A THR 88 A ALA 85 A ALA 71 A LEU 87 A LEU 73 B LEU 27 B LEU 13 B GLU 31 B GLU 17 B ALA 121 B ALA 107 B ASN 131 B ASN 117 B GLY 110 B GLY 96 B SER 117 B SER 103 B ILE 54 B ILE 40 B MET 59 B MET 45 B LYS 62 B LYS 48 B VAL 68 B VAL 54 B GLU 71 B GLU 57 B GLU 72 B GLU 58 B ASN 35 B ASN 21 B LYS 41 B LYS 27 B ASN 96 B ASN 82 B THR 102 B THR 88 B ALA 85 B ALA 71 B LEU 87 B LEU 73 152 P 31 2 1