1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0000-0002-1259-0082 Ramireddy, R.R. 0000-0002-1273-2829 Vidadala, V.N. 0000-0002-6655-0641 Chaubey, B. 0000-0001-6039-8434 Olsen, G.L. 0000-0001-6642-7144 Varani, G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C10 H15 N5 O7 P 1 348.229 n N1-PROTONATED ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C9 H15 N3 O8 P 1 324.204 n N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C24 H29 N7 O2 447.533 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE Palbociclib non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 R C Y 39 N N Y 40 N C Y 41 N N Y 42 N C Y 43 N C Y 44 N C N 45 N N Y 46 N N Y 47 N C Y 48 N N N 49 R C N 50 N O N 51 S C N 52 N O N 53 R C N 54 N O N 55 N C N 56 N O N 57 N O N 58 N O N 59 N P N 60 N O 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 O N 77 N P N 78 N O N 79 N O N 80 N O N 81 N C N 82 R C N 83 N O N 84 S C N 85 N O N 86 R C N 87 N O N 88 R C N 89 N N N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N C N 96 N C N 97 N H N 98 N H N 99 N H 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 H N 108 N H N 109 N H N 110 N H N 111 N O N 112 N P N 113 N O N 114 N O N 115 N O N 116 N C N 117 R C N 118 N O N 119 S C N 120 N O N 121 R C N 122 N O N 123 R C N 124 N N N 125 N C N 126 N O N 127 N N N 128 N C N 129 N N N 130 N C N 131 N C 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 H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N O N 148 N P N 149 N O N 150 N O N 151 N O N 152 N C N 153 R C N 154 N O N 155 S C N 156 N O N 157 R C N 158 N O N 159 R C Y 160 N N Y 161 N C Y 162 N N Y 163 N C N 164 N C N 165 N O N 166 N N N 167 N C N 168 N N N 169 N N Y 170 N C N 171 N H N 172 N H N 173 N H 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 H N 182 N H N 183 N H N 184 N H N 185 N O N 186 N C N 187 N C Y 188 N C Y 189 N C N 190 N C Y 191 N C Y 192 N C Y 193 N N Y 194 N C Y 195 N N Y 196 N C Y 197 N N N 198 N C N 199 N C N 200 N C N 201 N C N 202 N C Y 203 N C N 204 N O N 205 N N Y 206 N C Y 207 N N Y 208 N C Y 209 N C Y 210 N C Y 211 N C N 212 N N N 213 N C N 214 N C N 215 N N N 216 N C N 217 N C N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H 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 H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N O N 248 N P N 249 N O N 250 N O N 251 N O N 252 N C N 253 R C N 254 N O N 255 S C N 256 N O N 257 R C N 258 N O N 259 R C N 260 N N N 261 N C N 262 N O N 263 N N N 264 N C N 265 N O N 266 N C N 267 N C 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 H N 277 N H N 278 N H N 279 N H N 280 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing 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 sing N 22 N sing N 23 N sing N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing Y 44 N sing Y 45 N doub N 46 N sing Y 47 N doub N 48 N sing Y 49 N sing Y 50 N doub Y 51 N sing Y 52 N sing Y 53 N sing N 54 N sing N 55 N sing N 56 N sing Y 57 N doub Y 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 doub 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 doub 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 doub N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub 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 sing N 139 N sing N 140 N sing N 141 N doub N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N doub 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 doub 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 sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing 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 sing Y 177 N sing Y 178 N sing Y 179 N doub N 180 N sing Y 181 N sing N 182 N sing Y 183 N doub N 184 N doub 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 doub N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing Y 199 N doub Y 200 N sing N 201 N sing Y 202 N sing N 203 N sing N 204 N sing N 205 N sing Y 206 N sing Y 207 N doub Y 208 N doub N 209 N sing Y 210 N sing Y 211 N doub N 212 N sing Y 213 N sing Y 214 N sing N 215 N sing Y 216 N sing 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 sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N doub N 232 N sing N 233 N sing Y 234 N doub Y 235 N sing Y 236 N sing Y 237 N doub N 238 N sing Y 239 N sing N 240 N sing Y 241 N doub 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 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 sing N 259 N sing N 260 N sing N 261 N doub 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 sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N doub N 286 N sing N 287 N sing N 288 N sing N 289 N doub N 290 N sing N 291 N doub N 292 N sing N 293 N sing UK Nucleic Acids Res. NARHAD 0389 1362-4962 54 10.1093/nar/gkag129 41844361 Three-dimensional structure of the palbociclib-HIV TAR complex. 2026 0000-0001-6039-8434 0000-0001-6642-7144 10.2210/pdb9pdf/pdb pdb_00009pdf 10.13018/BMR31258 9325.569 RNA (29-MER) 1 syn polymer 447.533 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE 1 syn non-polymer no yes GGCAG(AP7)U(CH)UGAGCCUGGGGGCUCUCUGCC GGCAGAUCUGAGCCUGGGGGCUCUCUGCC A polyribonucleotide 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 -4.448 1 19 A 17 A 45 -1.556 A_G17:C45_A 1 4.513 -0.636 -0.255 -0.103 -0.306 1 19 A 18 A 44 4.876 A_G18:C44_A 2 -12.580 0.050 -0.070 -0.079 2.422 1 19 A 19 A 43 4.313 A_C19:G43_A 3 -14.548 0.180 0.093 -0.116 -3.727 1 20 A 20 A 42 -0.444 A_A20:U42_A 4 -17.953 0.048 0.099 -0.111 -7.263 1 19 A 21 A 41 -4.235 A_G21:C41_A 5 -10.814 -0.129 0.168 0.024 -6.091 1 19 A 26 A 39 3.842 A_G26:C39_A 6 -7.570 0.217 0.189 -0.052 -7.781 1 20 A 27 A 38 5.199 A_A27:U38_A 7 -9.337 -0.252 0.025 -0.231 -6.084 1 19 A 28 A 37 1.880 A_G28:C37_A 8 -9.520 0.191 -0.057 -0.152 6.033 1 19 A 29 A 36 -0.554 A_C29:G36_A 9 10.297 -0.322 -0.385 0.002 20.084 1 19 A 30 A 35 6.849 A_C30:G35_A 10 16.734 0.514 -0.354 -0.302 2.637 35.178 A A 17 18 14.518 A A 45 44 3.143 8.689 0.157 -1.739 AA_G17G18:C44C45_AA 1 0.589 -0.984 34.116 -4.040 -0.180 2.824 32.003 A A 18 19 10.153 A A 44 43 3.133 5.570 0.005 -1.548 AA_G18C19:G43C44_AA 2 -0.592 1.079 31.521 -3.732 -0.107 2.562 32.833 A A 19 20 18.725 A A 43 42 3.239 10.407 -0.144 -1.646 AA_C19A20:U42G43_AA 3 1.508 -2.713 31.147 -4.539 0.491 2.525 33.453 A A 20 21 20.470 A A 42 41 3.274 11.553 -0.022 -1.656 AA_A20G21:C41U42_AA 4 0.356 -0.631 31.447 -4.623 0.092 5.653 82.811 A A 21 26 7.226 A A 41 39 6.060 9.543 -0.877 -3.850 AA_G21G26:C39C41_AA 5 1.678 -1.270 82.344 -3.331 0.737 2.870 31.821 A A 26 27 8.459 A A 39 38 3.157 4.622 -0.140 -1.811 AA_G26A27:U38C39_AA 6 -0.184 0.337 31.492 -4.085 0.224 2.774 33.914 A A 27 28 12.387 A A 38 37 3.180 7.174 -0.204 -1.630 AA_A27G28:C37U38_AA 7 0.483 -0.834 33.165 -3.855 0.421 2.295 23.287 A A 28 29 15.488 A A 37 36 2.967 6.178 -0.311 -2.185 AA_G28C29:G36C37_AA 8 -0.352 0.883 22.461 -7.151 0.670 2.828 25.857 A A 29 30 8.202 A A 36 35 3.157 3.648 0.184 -1.803 AA_C29C30:G35G36_AA 9 -3.314 7.450 25.391 -4.967 -1.261 audit_author citation citation_author repository Initial release Database references Structure summary 1 0 2026-02-04 1 1 2026-04-08 _audit_author.name _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1R35GM126942 varani@uw.edu 0000-0001-6642-7144 Gabriele Varani principal investigator/group leader Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex N RCSB Y RCSB 2025-06-30 REL REL LQQ LQQ SUBJECT OF INVESTIGATION LQQ 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE 32630 synthetic construct sample 1 29 Y N structures with the lowest energy 200 12 isotropic 3 2D 1H-1H TOCSY isotropic 3 2D 1H-1H NOESY isotropic 3 2D 1H-1H TOCSY isotropic 3 2D 1H-1H NOESY isotropic 3 2D 1H-1H NOESY isotropic 3 2D 1H-1H TOCSY isotropic 3 2D 1H-13C HMQC isotropic 3 2D 1H-13C CT-HSQC aliphatic isotropic 3 2D 1H-13C CT-HSQC aromatic isotropic 3 2D 13C-filtered/edited NOESY isotropic 3 2D 1H-15N HSQC isotropic 3 2D 1H-15N HSQC NH2 only isotropic 3 2D 1H-1N HNNCOSY isotropic 3 2D 1H-15N SoFASTHMQC isotropic 3 2D 1H-13C HMQC isotropic 3 2D 1H-13C CT-HSQC aliphatic isotropic 3 2D 1H-13C CT-HSQC aromatic isotropic 3 2D 1H-15N HSQC NH2 only isotropic 3 2D 1H-13C HMQC isotropic 3 2D 1H-13C CT-HSQC aliphatic isotropic 3 2D 1H-13C CT-HSQC aromatic isotropic 3 2D 13C-filtered/edited NOESY isotropic 3 2D 1H-15N HSQC NH2 only isotropic 3 2D 1H-1H NOESY isotropic 3 2D 1H-1H NOESY 0.9 mM natural abundance 0.9 mM natural abundance 0.9 mM natural abundance 0.45 mM [U-99% 13C; U-99% 15N] 0.27 mM [U-13C; U-15N]-Ade 0.86 mM [U-13C; U-15N]-Cyt 0.9 mM [U-99% 2H] 0.45 mM [U-99% 13C; U-99% 15N] 0.27 mM [U-13C; U-15N]-Ade 0.8 mM [U-13C; U-15N]-Cyt 0.9 mM [U-99% 2H] Sample conditions to record exchangeable proton distance information (imino, amino) 20 mM bis tris d19, 50 mM sodium chloride mM low temperature 5.8 pH 1 atm 278 K Sample conditions to record non-exchangeable proton distance information. Same sample as id#1 buffer exchanged with 100% D2O containing d19 buffer 20 mM bis tris d19, 50 mM sodium chloride mM high temperature 5.8 pH 1 atm 310 K Sample conditions to record exchangeable proton distance information. Same sample as id#4 buffer exchanged with 95% H2O containing d19 buffer 20 mM bis tris d19, 50 mM sodium chloride mM low temperature 5.8 pH 1 atm 278 K Sample conditions to record exchangeable proton distance information. Same sample as id#6 buffer exchanged with 95% H2O containing d19 buffer 20 mM bis tris d19, 50 mM sodium chloride mM low temperature 5.8 pH 1 atm 278 K Sample conditions to record exchangeable proton distance information. Same sample as id#8 buffer exchanged with 95% H2O containing d19 buffer 20 mM bis tris d19, 50 mM sodium chloride mM low temperature 5.8 pH 1 atm 278 K Sample conditions to record exchangeable proton distance information. Same sample as id#10 buffer exchanged with 95% H2O containing d19 buffe 20 mM bis tris d19, 50 mM sodium chloride mM low temperature 5.8 pH 1 atm 278 K Sample conditions to record non-exchangeable proton distance information. Same sample as id#1 buffer exchanged with 100% D2O containing sodium acetate buffer 20 mM sodium acatate mM high temperature 5.0 pH 1 atm 310 K Sample conditions to record for identification of 13C of A, C, G and U. 20 mM sodium acatate mM high temperature 5.0 pH 1 atm 310 K Sample conditions to record for identification of 13C of A 20 mM sodium acatate mM high temperature 5.0 pH 1 atm 310 K Sample conditions to record for identification of 13C of C 20 mM sodium acatate mM high temperature 5.0 pH 1 atm 310 K Sample conditions to record non-exchangeable proton distance information and simplify the spectra by deuteration of ribose. 20 mM sodium acatate mM high temperature 5.0 pH 1 atm 310 K version 3.8 simulated annealing 1 lowest energy 0.9 mM HIV TAR RNA (29-MER), 90% H2O/10% D2O 1.8 mM Palbociclib (LQQ), 0.9 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 90%H2O/10%D2O HIV TAR RNA_Palbociclib_H2O complex 90% H2O/10% D2O solution 0.9 mM HIV TAR RNA (29-MER), 100% D2O 1.8 mM Palbociclib (LQQ), 0.9 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 100%D2O HIV TAR RNA_Palbociclib_D2O complex 100% D2O solution 0.9 mM HIV TAR RNA (29-MER), 100% D2O 1.8 mM Palbociclib (LQQ), 0.9 mM RNA (29-MER), 0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2O HIV TAR RNA_Palbociclib_D2O complex2 100% D2O solution 0.45 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER), 100% D2O 0.9 mM Palbociclib (LQQ), 0.45 mM RNA (29-MER), 0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2O 13C/15N_labeled_HIV TAR RNA_Palbociclib_D2O complex 100% D2O solution 0.27 mM [U-13C; U-15N]-Ade HIV TAR RNA (29-MER), 100% D2O 0.6 mM Palbociclib (LQQ), 0.27 mM RNA (29-MER), 0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2O 13C/15N_A only labeled_HIV TAR RNA_Palbociclib_D2O complex 100% D2O solution 0.86 mM [U-13C; U-15N]-Cyt HIV TAR RNA (29-MER), 100% D2O 1.8 mM Palbociclib (LQQ), 0.86 mM RNA (29-MER), 0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2O 13C/15N_C only labeled_HIV TAR RNA_Palbociclib_D2O complex 100% D2O solution 0.9 mM [U-99% 2H] HIV TAR RNA (29-MER), 100% D2O 1.8 mM Palbociclib (LQQ), 0.9 mM RNA (29-MER), 0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2O Partially 2H labeled_HIV TAR RNA_Palbociclib_D2O complex 100% D2O solution 0.45 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER), 95% H2O/5% D2O 0.9 mM Palbociclib (LQQ), 0.45 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 95%H2O/5%D2O 13C/15N_labeled_HIV TAR RNA_Palbociclib_H2O complex 95% H2O/5% D2O solution 0.27 mM [U-13C; U-15N]-Ade HIV TAR RNA (29-MER), 95% H2O/5% D2O 0.5 mM Palbociclib (LQQ), 0.27 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 95%H2O/5%D2O 13C/15N_A only labeled_HIV TAR RNA_Palbociclib_H2O complex 95% H2O/5% D2O solution 0.8 mM [U-13C; U-15N]-Cyt HIV TAR RNA (29-MER), 95% H2O/5% D2O 1.6 mM Palbociclib (LQQ), 0.8 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 95%H2O/5%D2O 13C/15N_C only labeled_HIV TAR RNA_Palbociclib_H2O complex 95% H2O/5% D2O solution 0.9 mM [U-99% 2H] HIV TAR RNA (29-MER), 95% H2O/5% D2O 1.6 mM Palbociclib (LQQ), 0.8 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 95%H2O/5%D2O Partially 2H labeled_HIV TAR RNA_Palbociclib_H2O complex 95% H2O/5% D2O solution Bruker Biospin collection TopSpin Schwieters, Kuszewski, Tjandra and Clore structure calculation X-PLOR NIH Bruker Biospin processing TopSpin Goddard peak picking Sparky Goddard chemical shift assignment Sparky Schwieters, Kuszewski, Tjandra and Clore refinement X-PLOR NIH 600 Bruker AVANCE II 700 Bruker AVANCE III 800 Bruker AVANCE III LQQ 117 2 LQQ LQQ 101 A GUA 17 n 1 G 17 A GUA 18 n 2 G 18 A CYT 19 n 3 C 19 A ADE 20 n 4 A 20 A GUA 21 n 5 G 21 A AP7 22 n 6 AP7 22 A URI 23 n 7 U 23 A CH 24 n 8 CH 24 A URI 25 n 9 U 25 A GUA 26 n 10 G 26 A ADE 27 n 11 A 27 A GUA 28 n 12 G 28 A CYT 29 n 13 C 29 A CYT 30 n 14 C 30 A URI 31 n 15 U 31 A GUA 32 n 16 G 32 A GUA 33 n 17 G 33 A GUA 34 n 18 G 34 A GUA 35 n 19 G 35 A GUA 36 n 20 G 36 A CYT 37 n 21 C 37 A URI 38 n 22 U 38 A CYT 39 n 23 C 39 A URI 40 n 24 U 40 A CYT 41 n 25 C 41 A URI 42 n 26 U 42 A GUA 43 n 27 G 43 A CYT 44 n 28 C 44 A CYT 45 n 29 C 45 A author_and_software_defined_assembly 1 monomeric not applicable NMR Distance Restraints A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C A CH 24 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 8 C 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 N Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex 1 N N 2 N N covale 1.612 both A G 21 A O3' G 5 1_555 A AP7 22 A P AP7 6 1_555 covale 1.608 both A AP7 22 A O3' AP7 6 1_555 A U 23 A P U 7 1_555 covale 1.609 both A U 23 A O3' U 7 1_555 A CH 24 A P CH 8 1_555 covale 1.608 both A CH 24 A O3' CH 8 1_555 A U 25 A P U 9 1_555 hydrog WATSON-CRICK A G 17 A N1 G 1 1_555 A C 45 A N3 C 29 1_555 hydrog WATSON-CRICK A G 17 A N2 G 1 1_555 A C 45 A O2 C 29 1_555 hydrog WATSON-CRICK A G 17 A O6 G 1 1_555 A C 45 A N4 C 29 1_555 hydrog WATSON-CRICK A G 18 A N1 G 2 1_555 A C 44 A N3 C 28 1_555 hydrog WATSON-CRICK A G 18 A N2 G 2 1_555 A C 44 A O2 C 28 1_555 hydrog WATSON-CRICK A G 18 A O6 G 2 1_555 A C 44 A N4 C 28 1_555 hydrog WATSON-CRICK A C 19 A N3 C 3 1_555 A G 43 A N1 G 27 1_555 hydrog WATSON-CRICK A C 19 A N4 C 3 1_555 A G 43 A O6 G 27 1_555 hydrog WATSON-CRICK A C 19 A O2 C 3 1_555 A G 43 A N2 G 27 1_555 hydrog WATSON-CRICK A A 20 A N1 A 4 1_555 A U 42 A N3 U 26 1_555 hydrog WATSON-CRICK A A 20 A N6 A 4 1_555 A U 42 A O4 U 26 1_555 hydrog WATSON-CRICK A G 21 A N1 G 5 1_555 A C 41 A N3 C 25 1_555 hydrog WATSON-CRICK A G 21 A N2 G 5 1_555 A C 41 A O2 C 25 1_555 hydrog WATSON-CRICK A G 21 A O6 G 5 1_555 A C 41 A N4 C 25 1_555 hydrog AP7-G MISPAIR A AP7 22 A N6 AP7 6 1_555 A G 26 A O6 G 10 1_555 hydrog CH-C MISPAIR A CH 24 A O2 CH 8 1_555 A C 29 A N4 C 13 1_555 hydrog CH-G MISPAIR A CH 24 A N4 CH 8 1_555 A G 36 A N7 G 20 1_555 hydrog U-A PAIR A U 25 A O4 U 9 1_555 A A 27 A N6 A 11 1_555 hydrog U-C MISPAIR A U 25 A O4 U 9 1_555 A C 37 A N4 C 21 1_555 hydrog WATSON-CRICK A G 26 A N1 G 10 1_555 A C 39 A N3 C 23 1_555 hydrog WATSON-CRICK A G 26 A N2 G 10 1_555 A C 39 A O2 C 23 1_555 hydrog WATSON-CRICK A G 26 A O6 G 10 1_555 A C 39 A N4 C 23 1_555 hydrog WATSON-CRICK A A 27 A N1 A 11 1_555 A U 38 A N3 U 22 1_555 hydrog WATSON-CRICK A A 27 A N6 A 11 1_555 A U 38 A O4 U 22 1_555 hydrog WATSON-CRICK A G 28 A N1 G 12 1_555 A C 37 A N3 C 21 1_555 hydrog WATSON-CRICK A G 28 A N2 G 12 1_555 A C 37 A O2 C 21 1_555 hydrog WATSON-CRICK A G 28 A O6 G 12 1_555 A C 37 A N4 C 21 1_555 hydrog WATSON-CRICK A C 29 A N3 C 13 1_555 A G 36 A N1 G 20 1_555 hydrog WATSON-CRICK A C 29 A N4 C 13 1_555 A G 36 A O6 G 20 1_555 hydrog WATSON-CRICK A C 29 A O2 C 13 1_555 A G 36 A N2 G 20 1_555 hydrog WATSON-CRICK A C 30 A N3 C 14 1_555 A G 35 A N1 G 19 1_555 hydrog WATSON-CRICK A C 30 A N4 C 14 1_555 A G 35 A O6 G 19 1_555 hydrog WATSON-CRICK A C 30 A O2 C 14 1_555 A G 35 A N2 G 19 1_555 RNA Palbociclib, complex, HIV-1 TAR, RNA, small molecule-RNA complex' 9PDF PDB 1 1 9PDF 17 45 9PDF 17 45 9PDF A 1 1 29