1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0009-0007-8991-5707 Fry, D.C. 0009-0002-2745-9340 Burk, M.J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID 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 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 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 C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N C N 7 N C N 8 N N N 9 N C N 10 N N N 11 N N N 12 N O N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N H N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N N N 29 S C N 30 N C N 31 N O N 32 N C N 33 N C N 34 N O N 35 N O N 36 N O N 37 N H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N N N 45 S C N 46 N C N 47 N O N 48 N C N 49 N C N 50 N C N 51 N O N 52 N O N 53 N O 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 N N 64 N C N 65 N C N 66 N O N 67 N O N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N N N 74 S C N 75 N C N 76 N O N 77 N C Y 78 N C Y 79 N N Y 80 N C Y 81 N C Y 82 N N N 83 N O 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 S C N 99 N C N 100 N C N 101 N C N 102 N O N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N N N 117 S C N 118 N C N 119 N O N 120 N C N 121 N C N 122 N C N 123 N C N 124 N O 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 H N 135 N H N 136 N H N 137 N H N 138 N N N 139 S C N 140 N C N 141 N O N 142 N C N 143 N C N 144 N C N 145 N C N 146 N N N 147 N O N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N N N 164 S C N 165 N C N 166 N O N 167 N C Y 168 N C Y 169 N C Y 170 N C Y 171 N C Y 172 N C Y 173 N C N 174 N O 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 H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N N N 187 S C N 188 N C N 189 N O N 190 N C N 191 N C N 192 N C N 193 N O 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 H N 202 N H N 203 N N N 204 S C N 205 N C N 206 N O N 207 N C N 208 N O N 209 N O N 210 N H 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 N N 218 S C N 219 N C N 220 N O N 221 N C Y 222 N C Y 223 N C Y 224 N C Y 225 N C Y 226 N C Y 227 N C N 228 N O N 229 N O N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N N N 242 S C N 243 N C N 244 N O N 245 N C N 246 N C N 247 N C N 248 N O N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N doub N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N doub N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N doub 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 doub 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 doub N 76 N sing N 77 N sing N 78 N sing N 79 N sing Y 80 N sing Y 81 N doub Y 82 N doub N 83 N sing Y 84 N sing N 85 N sing Y 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 doub 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 sing 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 doub N 118 N sing N 119 N sing 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 sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub 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 sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing 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 sing N 162 N doub N 163 N sing N 164 N sing N 165 N sing N 166 N sing Y 167 N doub Y 168 N sing Y 169 N sing N 170 N sing Y 171 N doub N 172 N sing Y 173 N doub N 174 N sing Y 175 N sing N 176 N sing 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 doub N 186 N sing N 187 N sing N 188 N sing N 189 N sing 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 sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N doub N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing 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 doub N 216 N sing N 217 N sing N 218 N sing N 219 N sing Y 220 N doub Y 221 N sing Y 222 N sing N 223 N sing Y 224 N doub N 225 N sing Y 226 N doub N 227 N sing Y 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 sing N 236 N sing N 237 N sing N 238 N sing N 239 N doub N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing US J.Am.Chem.Soc. JACSAT 1520-5126 147 32522 32536 10.1021/jacs.5c06142 40891737 Overcoming Immune Checkpoint Inhibitor Resistance with Potent, Selective Dual alpha v beta 6/8 Inhibitors Based on Engineered Lasso Peptides. 2025 0000-0002-2045-2691 10.2210/pdb9ny3/pdb pdb_00009ny3 10.13018/BMR31237 2301.603 LR4-488 peptide 1 man polymer no no GGRGHVPEYFVRGDLISFYK GGRGHVPEYFVRGDLISFYK A polypeptide(L) n n n n n n n n n n n n n n n n n n n n sample 1 20 32630 synthetic construct 562 Escherichia coli Biological sequence citation citation_author repository Initial release Database references 1 0 2025-04-02 1 1 2025-09-17 _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year Not funded david.fry@njbio.com 0009-0007-8991-5707 David Fry C principal investigator/group leader similar peptide LR4-488 peptide NMR structure N RCSB Y RCSB 2025-03-26 REL REL N structures with the lowest energy 40 15 isotropic 1 1D 1H isotropic 1 2D COSY isotropic 1 2D TOCSY (mix = 60 ms) isotropic 1 2D NOESY (mix = 200 ms) isotropic 1 2D 1H-15N sofastHMQC 2.56 mM uniform 15N 0 Not defined conditions_1 5 2 pH 1 atm 297 1 K molecular dynamics 1 lowest energy 2.56 mM uniform 15N LR4-488, 93% H2O/7% D2O LR4-488 93% H2O/7% D2O solution Bruker data analysis TopSpin Delaglio and Kuszewski structure calculation DYNAMO 700 Bruker AVANCE NEO GLY 1 n 1 GLY 1 A GLY 2 n 2 GLY 2 A ARG 3 n 3 ARG 3 A GLY 4 n 4 GLY 4 A HIS 5 n 5 HIS 5 A VAL 6 n 6 VAL 6 A PRO 7 n 7 PRO 7 A GLU 8 n 8 GLU 8 A TYR 9 n 9 TYR 9 A PHE 10 n 10 PHE 10 A VAL 11 n 11 VAL 11 A ARG 12 n 12 ARG 12 A GLY 13 n 13 GLY 13 A ASP 14 n 14 ASP 14 A LEU 15 n 15 LEU 15 A ILE 16 n 16 ILE 16 A SER 17 n 17 SER 17 A PHE 18 n 18 PHE 18 A TYR 19 n 19 TYR 19 A LYS 20 n 20 LYS 20 A author_and_software_defined_assembly 1 monomeric not applicable NMR Distance Restraints 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 1_555 x,y,z identity operation 0.0 0.0 0.0 A N VAL 6 A N VAL 6 A O TYR 19 A O TYR 19 1 A OE2 GLU 8 A OE2 GLU 8 1 Y 2 A OE2 GLU 8 A OE2 GLU 8 1 Y 3 A OE2 GLU 8 A OE2 GLU 8 1 Y 4 A OE2 GLU 8 A OE2 GLU 8 1 Y 5 A OE2 GLU 8 A OE2 GLU 8 1 Y 6 A OE2 GLU 8 A OE2 GLU 8 1 Y 7 A OE2 GLU 8 A OE2 GLU 8 1 Y 8 A OE2 GLU 8 A OE2 GLU 8 1 Y 9 A OE2 GLU 8 A OE2 GLU 8 1 Y 10 A OE2 GLU 8 A OE2 GLU 8 1 Y 11 A OE2 GLU 8 A OE2 GLU 8 1 Y 12 A OE2 GLU 8 A OE2 GLU 8 1 Y 13 A OE2 GLU 8 A OE2 GLU 8 1 Y 14 A OE2 GLU 8 A OE2 GLU 8 1 Y 15 A OE2 GLU 8 A OE2 GLU 8 1 Y 1 A A N CD GLY GLU 1 8 1.39 2 A A N CD GLY GLU 1 8 1.37 3 A A N CD GLY GLU 1 8 1.37 4 A A N CD GLY GLU 1 8 1.37 5 A A N CD GLY GLU 1 8 1.38 5 A A OE1 C GLU SER 8 17 1.99 6 A A N CD GLY GLU 1 8 1.39 6 A A O O ARG PHE 3 18 2.15 7 A A N CD GLY GLU 1 8 1.37 8 A A N CD GLY GLU 1 8 1.44 9 A A N CD GLY GLU 1 8 1.41 10 A A N CD GLY GLU 1 8 1.40 10 A A N O GLY PHE 1 18 1.90 11 A A N CD GLY GLU 1 8 1.39 12 A A N CD GLY GLU 1 8 1.39 13 A A N CD GLY GLU 1 8 1.38 13 A A H1 O GLY PHE 1 18 1.58 14 A A N CD GLY GLU 1 8 1.39 15 A A N CD GLY GLU 1 8 1.39 5 A SER 17 12.77 5 A A ARG GLY 3 4 106.36 11 A A GLY HIS 4 5 142.76 1 A TYR 9 0.081 SIDE CHAIN 6 A ARG 12 0.094 SIDE CHAIN 9 A ARG 3 0.094 SIDE CHAIN 12 A ARG 12 0.113 SIDE CHAIN 13 A TYR 9 0.067 SIDE CHAIN 3 -3.91 0.60 121.00 117.09 A A A CB CG CD2 TYR TYR TYR 19 19 19 N 3 3.99 0.60 121.00 124.99 A A A CB CG CD1 TYR TYR TYR 19 19 19 N 4 -3.65 0.60 121.00 117.35 A A A CB CG CD2 TYR TYR TYR 19 19 19 N 5 -3.91 0.60 121.00 117.09 A A A CB CG CD2 TYR TYR TYR 19 19 19 N 5 3.74 0.60 121.00 124.74 A A A CB CG CD1 TYR TYR TYR 19 19 19 N 11 3.98 0.60 121.00 124.98 A A A CB CG CD2 TYR TYR TYR 19 19 19 N 11 -4.02 0.60 121.00 116.98 A A A CB CG CD1 TYR TYR TYR 19 19 19 N 12 3.11 0.50 120.30 123.41 A A A NE CZ NH2 ARG ARG ARG 12 12 12 N 14 4.10 0.60 121.00 125.10 A A A CB CG CD2 TYR TYR TYR 19 19 19 N 14 -4.03 0.60 121.00 116.97 A A A CB CG CD1 TYR TYR TYR 19 19 19 N 8 A A CB CG GLU GLU 8 8 0.124 0.019 1.517 1.641 N 8 A A CG CD GLU GLU 8 8 0.129 0.015 1.515 1.644 N 1 A HIS 5 -146.56 30.36 2 A HIS 5 -167.57 -62.11 2 A VAL 11 66.03 113.64 2 A LEU 15 47.91 102.80 3 A HIS 5 -148.13 45.06 3 A PRO 7 -38.65 119.30 3 A PHE 10 -41.71 152.13 3 A LEU 15 60.59 176.41 4 A GLU 8 -61.47 -158.74 4 A TYR 9 -44.26 150.04 4 A ARG 12 68.61 171.81 4 A ASP 14 50.46 -162.88 5 A ARG 3 -105.77 46.31 5 A HIS 5 -164.61 -77.63 5 A TYR 9 -64.39 -166.93 6 A ARG 3 67.85 177.47 6 A HIS 5 -145.84 37.91 6 A PRO 7 -39.23 108.27 6 A TYR 9 65.09 175.58 6 A ARG 12 70.84 94.64 6 A ASP 14 -78.51 -164.67 6 A ILE 16 62.08 109.28 7 A HIS 5 -173.70 -56.90 7 A PHE 10 -74.58 -97.71 7 A ASP 14 -72.75 -155.64 7 A LEU 15 -46.99 168.24 7 A PHE 18 -166.41 115.94 8 A PRO 7 -39.31 124.92 8 A PHE 10 67.50 96.44 8 A ASP 14 -60.50 -171.50 9 A HIS 5 -151.98 40.67 9 A PRO 7 -39.16 115.59 9 A TYR 9 -57.03 -7.91 9 A ARG 12 -107.09 77.72 10 A ARG 3 -91.47 55.33 10 A HIS 5 -170.10 -56.62 10 A PRO 7 -44.38 92.22 10 A TYR 9 52.35 -153.74 10 A PHE 10 -154.49 19.29 10 A ASP 14 61.59 112.98 10 A LEU 15 65.94 174.12 10 A TYR 19 -41.39 162.47 11 A HIS 5 -165.70 -42.92 11 A ARG 12 -170.54 55.20 11 A ASP 14 -56.28 -175.23 12 A HIS 5 -166.67 -57.61 12 A VAL 11 65.32 171.01 12 A ARG 12 65.58 80.60 13 A PHE 10 -168.16 22.58 13 A VAL 11 51.16 -165.02 13 A ASP 14 48.03 -158.77 14 A HIS 5 -149.77 -78.04 14 A ARG 12 -170.50 55.18 14 A ASP 14 -56.32 -175.22 15 A PRO 7 -36.96 118.21 15 A TYR 9 45.07 -159.87 15 A PHE 10 66.83 110.18 15 A ASP 14 81.82 -174.92 15 A LEU 15 52.65 100.74 15 A SER 17 60.90 108.41 N LR4-488 peptide NMR structure 1 N N DE NOVO PROTEIN lasso, designed, de novo protein 9NY3 PDB 1 1 9NY3 1 20 9NY3 1 20 9NY3 A 1 1 20 2 anti-parallel A VAL 6 A VAL 6 A PRO 7 A PRO 7 A PHE 18 A PHE 18 A TYR 19 A TYR 19