Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T44458 | Target Info | |||
| Target Name | Cyclin-dependent kinase 9 (CDK9) | ||||
| Synonyms | Tat-associated kinase complex catalytic subunit; TAK; Similar to cyclin-dependent kinase 9; Serine/threonine-protein kinase PITALRE; Cyclin-dependent protein kinase Cdk9; Cell division protein kinase 9; Cell division cycle 2-like protein kinase 4; CDC2L4; CDC2-related kinase; C-2K | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | CDK9 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Adenosine monophosphate | Ligand Info | |||||
| Structure Description | The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat | PDB:4IMY | ||||
| Method | X-ray diffraction | Resolution | 2.94 Å | Mutation | No | [1] |
| PDB Sequence |
VECPFCDEVS
17 KYEKLAKIGQ27 GTFGEVFKAR37 HRKTGQKVAL47 KKVLMENEKE57 GFPITALREI 67 KILQLLKHEN77 VVNLIEICRT87 KGSIYLVFDF105 CEHDLAGLLS115 NVLVKFTLSE 125 IKRVMQMLLN135 GLYYIHRNKI145 LHRDMKAANV155 LITRDGVLKL165 ADFGLARAFS 175 LAKNSQPNRY185 NRVVTLWYRP196 PELLLGERDY206 GPPIDLWGAG216 CIMAEMWTRS 226 PIMQGNTEQH236 QLALISQLCG246 SITPEVWPNV256 DNYELYEKLE266 LVKGQKRKVK 276 DRLKAYVRDP286 YALDLIDKLL296 VLDPAQRIDS306 DDALNHDFFW316 SDPMPSDLKG 326 MLST
|
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ILE25
2.705
VAL33
3.512
ALA46
2.909
LYS48
1.936
GLU66
2.514
LEU70
2.457
VAL79
2.433
ASN80
4.828
LEU101
4.298
PHE103
2.152
ASP104
2.184
|
|||||
| Ligand Name: Adenosine | Ligand Info | |||||
| Structure Description | crystal structure of P-TEFb complex with AFF4 and Tat | PDB:4OGR | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [2] |
| PDB Sequence |
VECPFCDEVS
17 KYEKLAKIGQ27 GTFGEVFKAR37 HRKTGQKVAL47 KKVLMENEKE57 GFPITALREI 67 KILQLLKHEN77 VVNLIEICRT87 KGSIYLVFDF105 CEHDLAGLLS115 NVLVKFTLSE 125 IKRVMQMLLN135 GLYYIHRNKI145 LHRDMKAANV155 LITRDGVLKL165 ADFGLARAFS 175 LAKNSQPNRY185 NRVVTLWYRP196 PELLLGERDY206 GPPIDLWGAG216 CIMAEMWTRS 226 PIMQGNTEQH236 QLALISQLCG246 SITPEVWPNV256 DNYELYEKLE266 LVKGQKRKVK 276 DRLKAYVRDP286 YALDLIDKLL296 VLDPAQRIDS306 DDALNHDFFW316 SDPMPSDLKG 326 MLST
|
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| Ligand Name: Adenosine triphosphate | Ligand Info | |||||
| Structure Description | Crystal Structure of Human CDK9/cyclinT1 in Complex with ATP | PDB:3BLQ | ||||
| Method | X-ray diffraction | Resolution | 2.90 Å | Mutation | Yes | [3] |
| PDB Sequence |
SVECPFCDEV
16 SKYEKLAKIG26 QGTFGEVFKA36 RHRKTGQKVA46 LKKVLMENEK56 EGFPITALRE 66 IKILQLLKHE76 NVVNLIEICR86 TSIYLVFDFC106 EHDLAGLLSN116 VLVKFTLSEI 126 KRVMQMLLNG136 LYYIHRNKIL146 HRDMKAANVL156 ITRDGVLKLA166 DFGLARAFSN 183 RYNRVVTLWY194 RPPELLLGER204 DYGPPIDLWG214 AGCIMAEMWT224 RSPIMQGNTE 234 QHQLALISQL244 CGSITPEVWP254 NVDNYELYEK264 LELVVKDRLK280 AYVRDPYALD 290 LIDKLLVLDP300 AQRIDSDDAL310 NHDFFWSDPM320 PSDLK
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ATP or .ATP2 or .ATP3 or :3ATP;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:28 or .A:29 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:109 or .A:149 or .A:151 or .A:154 or .A:156 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Flavopiridol | Ligand Info | |||||
| Structure Description | Crystal Structure of Human CDK9/cyclinT1 in complex with Flavopiridol | PDB:3BLR | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | Yes | [3] |
| PDB Sequence |
SVECPFCDEV
16 SKYEKLAKIG26 QGTFGEVFKA36 RHRKTGQKVA46 LKKVLMENEK56 EGFPITALRE 66 IKILQLLKHE76 NVVNLIEICR86 TSIYLVFDFC106 EHDLAGLLSN116 VLVKFTLSEI 126 KRVMQMLLNG136 LYYIHRNKIL146 HRDMKAANVL156 ITRDGVLKLA166 DFGLARAFSL 176 APNRYNRVVT191 LWYRPPELLL201 GERDYGPPID211 LWGAGCIMAE221 MWTRSPIMQG 231 NTEQHQLALI241 SQLCGSITPE251 VWPNVDNYEL261 YEKLELVKVK276 DRLKAYVRDP 286 YALDLIDKLL296 VLDPAQRIDS306 DDALNHDFFW316 SDPMPSDLKG326 |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CPB or .CPB2 or .CPB3 or :3CPB;style chemicals stick;color identity;select .A:25 or .A:26 or .A:30 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:151 or .A:153 or .A:154 or .A:156 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: AZD4573 | Ligand Info | |||||
| Structure Description | CDK9-Cyclin-T1 complex bound by compound 24 | PDB:6Z45 | ||||
| Method | X-ray diffraction | Resolution | 3.37 Å | Mutation | No | [4] |
| PDB Sequence |
YDDNECPFCD
14 EVSKYEKLAK24 IGQGTFGEVF34 KARHRKTGQR44 VALKKVLMEN54 EKEGFPITAL 64 REIKILQLLK74 HENVVNLIEI84 CRTKCKGSIY100 LVFDFCEHDL110 AGLLSNVLVK 120 FTLSEIKRVM130 QMLLNGLFYI140 HRNKILHRDM150 KAANVLITRD160 GVLKLADFGL 170 ARAFSLNPNR184 YNRVVTLWYR195 PPELLLGERD205 YGPPIDLWGA215 GCIMAEMWTR 225 SPIMQGNTEQ235 HQLALISQLC245 GSITPEVWPN255 VDNYELYEKL265 ELVKGQKRKV 275 KDRLAAYVRD285 PYALDLIDKL295 LVLDPAQRID305 SEDALEHDFF315 WSDPMPSDLK 325 GML
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .Q6E or .Q6E2 or .Q6E3 or :3Q6E;style chemicals stick;color identity;select .A:23 or .A:24 or .A:25 or .A:30 or .A:33 or .A:35 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:153 or .A:154 or .A:156 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ALA23
4.023
LYS24
4.774
ILE25
3.359
PHE30
4.974
VAL33
3.650
LYS35
3.828
ALA46
3.507
LYS48
4.095
VAL79
3.398
PHE103
3.249
ASP104
3.577
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| Ligand Name: AMP-PNP | Ligand Info | |||||
| Structure Description | Crystal structure of HIV-1 Tat complexed with ATP-bound human P-TEFb | PDB:3MIA | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | Yes | [5] |
| PDB Sequence |
VECPFCDEVS
17 KYEKLAKIGQ27 GTFGEVFKAR37 HRKTGQKVAL47 KKVLMENEKE57 GFPITALREI 67 KILQLLKHEN77 VVNLIEICRT87 KGSIYLVFDF105 CEHDLAGLLS115 NVLVKFTLSE 125 IKRVMQMLLN135 GLYYIHRNKI145 LHRDMKAANV155 LITRDGVLKL165 ADFGLARAFS 175 LAKNSQPNRY185 NRVVTLWYRP196 PELLLGERDY206 GPPIDLWGAG216 CIMAEMWTRS 226 PIMQGNTEQH236 QLALISQLCG246 SITPEVWPNV256 DNYELYEKLE266 LVKGQKRKVK 276 DRLKAYVRDP286 YALDLIDKLL296 VLDPAQRIDS306 DDALNHDFFW316 SDPMPSDLKG 326 MLSTHLTSMF336 EYLA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ANP or .ANP2 or .ANP3 or :3ANP;style chemicals stick;color identity;select .A:25 or .A:32 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:109 or .A:153 or .A:154 or .A:156 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole | Ligand Info | |||||
| Structure Description | Structure of CDK9/cyclinT1 in complex with DRB | PDB:3MY1 | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | Yes | [6] |
| PDB Sequence |
DSVECPFCDE
15 VSKYEKLAKI25 GQGTFGEVFK35 ARHRKTGQKV45 ALKKVLMENE55 KEGFPITALR 65 EIKILQLLKH75 ENVVNLIEIC85 RTKKGSIYLV102 FDFCEHDLAG112 LLSNVLVKFT 122 LSEIKRVMQM132 LLNGLYYIHR142 NKILHRDMKA152 ANVLITRDGV162 LKLADFGLAR 172 AFSLAKNSQP182 NRYNRVVTLW193 YRPPELLLGE203 RDYGPPIDLW213 GAGCIMAEMW 223 TRSPIMQGNT233 EQHQLALISQ243 LCGSITPEVW253 PNVDNYELYE263 KLELVKGQKR 273 KVKDRLKAYV283 RDPYALDLID293 KLLVLDPAQR303 IDSDDALNHD313 FFWSDPMPSD 323 LKGM
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .RFZ or .RFZ2 or .RFZ3 or :3RFZ;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:30 or .A:31 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:109 or .A:153 or .A:154 or .A:156 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Phosphonothreonine | Ligand Info | |||||
| Structure Description | Crystal Structure of Human CDK9/cyclinT1 in complex with Flavopiridol | PDB:3BLR | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | Yes | [3] |
| PDB Sequence |
SVECPFCDEV
16 SKYEKLAKIG26 QGTFGEVFKA36 RHRKTGQKVA46 LKKVLMENEK56 EGFPITALRE 66 IKILQLLKHE76 NVVNLIEICR86 TSIYLVFDFC106 EHDLAGLLSN116 VLVKFTLSEI 126 KRVMQMLLNG136 LYYIHRNKIL146 HRDMKAANVL156 ITRDGVLKLA166 DFGLARAFSL 176 APNRYNRVVT191 LWYRPPELLL201 GERDYGPPID211 LWGAGCIMAE221 MWTRSPIMQG 231 NTEQHQLALI241 SQLCGSITPE251 VWPNVDNYEL261 YEKLELVKVK276 DRLKAYVRDP 286 YALDLIDKLL296 VLDPAQRIDS306 DDALNHDFFW316 SDPMPSDLKG326 |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .A:148 or .A:172 or .A:184 or .A:185 or .A:187 or .A:188 or .A:189 or .A:204 or .A:206; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 4-(thiazol-5-yl)-pyrimidine derivative 1 | Ligand Info | |||||
| Structure Description | Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor | PDB:4BCJ | ||||
| Method | X-ray diffraction | Resolution | 3.16 Å | Mutation | Yes | [7] |
| PDB Sequence |
DSVECPFCDE
15 VSKYEKLAKI25 GQGTFGEVFK35 ARHRKTGQKV45 ALKKVLMENE55 KEGFPITALR 65 EIKILQLLKH75 ENVVNLIEIC85 RTKKGSIYLV102 FDFCEHDLAG112 LLSNVLVKFT 122 LSEIKRVMQM132 LLNGLYYIHR142 NKILHRDMKA152 ANVLITRDGV162 LKLADFGLAR 172 AFSLAPNRYN187 RVVTLWYRPP197 ELLLGERDYG207 PPIDLWGAGC217 IMAEMWTRSP 227 IMQGNTEQHQ237 LALISQLCGS247 ITPEVWPNVD257 NYELYEKLEL267 VKGQKRKVKD 277 RLKAYVRDPY287 ALDLIDKLLV297 LDPAQRIDSD307 DALNHDFFWS317 DPMPSDLKG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .T9N or .T9N2 or .T9N3 or :3T9N;style chemicals stick;color identity;select .A:25 or .A:30 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:154 or .A:156 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: L-serine-O-phosphate | Ligand Info | |||||
| Structure Description | Crystal Structure of Human CDK9/cyclinT1 in complex with MC180295 | PDB:6W9E | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | Yes | [8] |
| PDB Sequence |
SVECPFCDEV
16 SKYEKLAKIG26 QGTFGEVFKA36 RHRKTGQKVA46 LKKVLMENEK56 EGFPITALRE 66 IKILQLLKHE76 NVVNLIEICR86 TKASKGSIYL101 VFDFCEHDLA111 GLLSNVLVKF 121 TLSEIKRVMQ131 MLLNGLYYIH141 RNKILHRDMK151 AANVLITRDG161 VLKLADFGLA 171 RAFSLQPNRY185 NRVVTLWYRP196 PELLLGERDY206 GPPIDLWGAG216 CIMAEMWTRS 226 PIMQGNTEQH236 QLALISQLCG246 SITPEVWPNV256 DNYELYEKLE266 LVKGQKRKVK 276 DRLKAYVRDP286 YALDLIDKLL296 VLDPAQRIDD307 DALNHDFFWS317 DPMPSDLKG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SEP or .SEP2 or .SEP3 or :3SEP;style chemicals stick;color identity;select .A:134 or .A:137 or .A:138 or .A:141 or .A:142 or .A:208 or .A:212 or .A:304 or .A:305 or .A:307 or .A:308 or .A:309 or .A:310; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[(E)-(3,5-Diamino-1h-Pyrazol-4-Yl)diazenyl]phenol | Ligand Info | |||||
| Structure Description | CDK9/cyclin T in complex with CAN508 | PDB:3TN8 | ||||
| Method | X-ray diffraction | Resolution | 2.95 Å | Mutation | Yes | [9] |
| PDB Sequence |
VECPFCDEVS
17 KYEKLAKIGQ27 GTFGEVFKAR37 HRKTGQKVAL47 KKVLMENEKE57 GFPITALREI 67 KILQLLKHEN77 VVNLIEICRT87 GSIYLVFDFC106 EHDLAGLLSN116 VLVKFTLSEI 126 KRVMQMLLNG136 LYYIHRNKIL146 HRDMKAANVL156 ITRDGVLKLA166 DFGLARAFSL 176 QPNRYNRVVT191 LWYRPPELLL201 GERDYGPPID211 LWGAGCIMAE221 MWTRSPIMQG 231 NTEQHQLALI241 SQLCGSITPE251 VWPNVDNYEL261 YEKLELVKGQ271 KRKVKDRLKA 281 YVRDPYALDL291 IDKLLVLDPA301 QRIDSDDALN311 HDFFWSDPMP321 SDLK |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .F18 or .F182 or .F183 or :3F18;style chemicals stick;color identity;select .A:25 or .A:26 or .A:33 or .A:46 or .A:48 or .A:66 or .A:70 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:156 or .A:166 or .A:167 or .A:168 or .A:169; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 4-(4-Methyl-2-Methylimino-3h-1,3-Thiazol-5-Yl)-2-[(4-Methyl-3-Morpholin-4-Ylsulfonyl-Phenyl)amino]pyrimidine-5-Carbonitrile | Ligand Info | |||||
| Structure Description | Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor | PDB:4BCH | ||||
| Method | X-ray diffraction | Resolution | 2.96 Å | Mutation | Yes | [7] |
| PDB Sequence |
SVECPFCDEV
16 SKYEKLAKIG26 QGTFGEVFKA36 RHRKTGQKVA46 LKKVLMENEK56 EGFPITALRE 66 IKILQLLKHE76 NVVNLIEICR86 TKAGSIYLVF103 DFCEHDLAGL113 LSNVLVKFTL 123 SEIKRVMQML133 LNGLYYIHRN143 KILHRDMKAA153 NVLITRDGVL163 KLADFGLARA 173 FSLPNRYNRV189 VTLWYRPPEL199 LLGERDYGPP209 IDLWGAGCIM219 AEMWTRSPIM 229 QGNTEQHQLA239 LISQLCGSIT249 PEVWPNVDNY259 ELYEKLELVK269 GQKRKVKDRL 279 KAYVRDPYAL289 DLIDKLLVLD299 PAQRIDSDDA309 LNHDFFWSDP319 MPSDLKGM |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .T7Z or .T7Z2 or .T7Z3 or :3T7Z;style chemicals stick;color identity;select .A:25 or .A:26 or .A:30 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:153 or .A:154 or .A:156 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2S)-2-[[9-propan-2-yl-6-[[4-(2-pyridinyl)phenyl]methylamino]-2-purinyl]amino]-1-butanol | Ligand Info | |||||
| Structure Description | Structure of CDK9/CyclinT in complex with S-CR8 | PDB:3LQ5 | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | Yes | [10] |
| PDB Sequence |
DSVECPFCDE
15 VSKYEKLAKI25 GQFGEVFKAR37 HRKTGQKVAL47 KKVLMENEKE57 GFPITALREI 67 KILQLLKHEN77 VVNLIEICRT87 KGSIYLVFDF105 CEHDLAGLLS115 NVLVKFTLSE 125 IKRVMQMLLN135 GLYYIHRNKI145 LHRDMKAANV155 LITRDGVLKL165 ADFGLARAFS 175 LAPNRYNRVV190 TLWYRPPELL200 LGERDYGPPI210 DLWGAGCIMA220 EMWTRSPIMQ 230 GNTEQHQLAL240 ISQLCGSITP250 EVWPNVDNYE260 LYEKLELVKG270 QKRKVKDRLK 280 AYVRDPYALD290 LIDKLLVLDP300 AQRIDSDDAL310 NHDFFWSDPM320 PSDLKGM |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SLQ or .SLQ2 or .SLQ3 or :3SLQ;style chemicals stick;color identity;select .A:23 or .A:24 or .A:25 or .A:26 or .A:27 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:153 or .A:154 or .A:156 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ALA23
4.020
LYS24
3.726
ILE25
3.553
GLY26
3.823
GLN27
3.758
VAL33
4.121
ALA46
3.437
LYS48
4.423
VAL79
3.223
PHE103
3.496
ASP104
3.633
|
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| Ligand Name: 2-[[3-(4-Ethanoyl-1,4-Diazepan-1-Yl)phenyl]amino]-4-[4-Methyl-2-(Methylamino)-1,3-Thiazol-5-Yl]pyrimidine-5-Carbonitrile | Ligand Info | |||||
| Structure Description | Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor | PDB:4BCF | ||||
| Method | X-ray diffraction | Resolution | 3.01 Å | Mutation | Yes | [7] |
| PDB Sequence |
DSVECPFCDE
15 VSKYEKLAKI25 GQGTFGEVFK35 ARHRKTGQKV45 ALKKVLMENE55 KEGFPITALR 65 EIKILQLLKH75 ENVVNLIEIC85 RTKASIYLVF103 DFCEHDLAGL113 LSNVLVKFTL 123 SEIKRVMQML133 LNGLYYIHRN143 KILHRDMKAA153 NVLITRDGVL163 KLADFGLARA 173 FSLPNRYNRV189 VTLWYRPPEL199 LLGERDYGPP209 IDLWGAGCIM219 AEMWTRSPIM 229 QGNTEQHQLA239 LISQLCGSIT249 PEVWPNVDNY259 ELYEKLELVK269 GQKRKVKDRL 279 KAYVRDPYAL289 DLIDKLLVLD299 PAQRIDSDDA309 LNHDFFWSDP319 MPSDLKG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .T6Q or .T6Q2 or .T6Q3 or :3T6Q;style chemicals stick;color identity;select .A:25 or .A:30 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:111 or .A:153 or .A:154 or .A:156 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-{[3-(1,4-Diazepan-1-yl)phenyl]amino}-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile | Ligand Info | |||||
| Structure Description | Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor | PDB:4BCG | ||||
| Method | X-ray diffraction | Resolution | 3.08 Å | Mutation | Yes | [11] |
| PDB Sequence |
SVECPFCDEV
16 SKYEKLAKIG26 QGTFGEVFKA36 RHRKTGQKVA46 LKKVLMENEK56 EGFPITALRE 66 IKILQLLKHE76 NVVNLIEICR86 TKGSIYLVFD104 FCEHDLAGLL114 SNVLVKFTLS 124 EIKRVMQMLL134 NGLYYIHRNK144 ILHRDMKAAN154 VLITRDGVLK164 LADFGLARAF 174 SLAKNSQPNR184 YNRVVTLWYR195 PPELLLGERD205 YGPPIDLWGA215 GCIMAEMWTR 225 SPIMQGNTEQ235 HQLALISQLC245 GSITPEVWPN255 VDNYELYEKL265 ELVKGQKRKV 275 KDRLKAYVRD285 PYALDLIDKL295 LVLDPAQRID305 SDDALNHDFF315 WSDPMPSDLK 325 GM
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .T3C or .T3C2 or .T3C3 or :3T3C;style chemicals stick;color identity;select .A:25 or .A:29 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:153 or .A:154 or .A:156 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 3-[[5-Cyano-4-[4-Methyl-2-(Methylamino)-1,3-Thiazol-5-Yl]pyrimidin-2-Yl]amino]benzenesulfonamide | Ligand Info | |||||
| Structure Description | Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor | PDB:4BCI | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | Yes | [7] |
| PDB Sequence |
YDSVECPFCD
14 EVSKYEKLAK24 IGQGTFGEVF34 KARHRKTGQK44 VALKKVLMEN54 EKEGFPITAL 64 REIKILQLLK74 HENVVNLIEI84 CRTGSIYLVF103 DFCEHDLAGL113 LSNVLVKFTL 123 SEIKRVMQML133 LNGLYYIHRN143 KILHRDMKAA153 NVLITRDGVL163 KLADFGLARA 173 FSLAPNRYNR188 VVTLWYRPPE198 LLLGERDYGP208 PIDLWGAGCI218 MAEMWTRSPI 228 MQGNTEQHQL238 ALISQLCGSI248 TPEVWPNVDN258 YELYEKLELV268 KGQKRKVKDR 278 LKAYVRDPYA288 LDLIDKLLVL298 DPAQRIDSDD308 ALNHDFFWSD318 PMPSDLKG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .T3E or .T3E2 or .T3E3 or :3T3E;style chemicals stick;color identity;select .A:25 or .A:30 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:154 or .A:156 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-((1R,3R)-3-(7-(4-fluoro-2-methoxyphenyl)-3H-imidazo[4,5-b]pyridin-2-yl)cyclopentyl)acetamide | Ligand Info | |||||
| Structure Description | Crystal structure of CDK9-Cyclin T1 bound by compound 6 | PDB:7NWK | ||||
| Method | X-ray diffraction | Resolution | 2.81 Å | Mutation | No | [12] |
| PDB Sequence |
SVECPFCDEV
16 SKYEKLAKIG26 QGFGEVFKAR37 HRKTGQKVAL47 KKVLMENEKE57 GFPITALREI 67 KILQLLKHEN77 VVNLIEICRT87 KGSIYLVFDF105 CEHDLAGLLS115 NVLVKFTLSE 125 IKRVMQMLLN135 GLYYIHRNKI145 LHRDMKAANV155 LITRDGVLKL165 ADFGLARAFS 175 LPNRYNRVVT191 LWYRPPELLL201 GERDYGPPID211 LWGAGCIMAE221 MWTRSPIMQG 231 NTEQHQLALI241 SQLCGSITPE251 VWPNVDNLVK269 GQKRKVKDRL279 KAYVRDPYAL 289 DLIDKLLVLD299 PAQRIDSDDA309 LNHDFFWSDP319 MPSDLKG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UT5 or .UT52 or .UT53 or :3UT5;style chemicals stick;color identity;select .A:25 or .A:27 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:153 or .A:154 or .A:156 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (4-amino-2-{[(1R,2R,4S)-bicyclo[2.2.1]heptan-2-yl]amino}-1,3-thiazol-5-yl)(2-nitrophenyl)methanone | Ligand Info | |||||
| Structure Description | Crystal Structure of Human CDK9/cyclinT1 in complex with MC180295 | PDB:6W9E | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | Yes | [8] |
| PDB Sequence |
SVECPFCDEV
16 SKYEKLAKIG26 QGTFGEVFKA36 RHRKTGQKVA46 LKKVLMENEK56 EGFPITALRE 66 IKILQLLKHE76 NVVNLIEICR86 TKASKGSIYL101 VFDFCEHDLA111 GLLSNVLVKF 121 TLSEIKRVMQ131 MLLNGLYYIH141 RNKILHRDMK151 AANVLITRDG161 VLKLADFGLA 171 RAFSLQPNRY185 NRVVTLWYRP196 PELLLGERDY206 GPPIDLWGAG216 CIMAEMWTRS 226 PIMQGNTEQH236 QLALISQLCG246 SITPEVWPNV256 DNYELYEKLE266 LVKGQKRKVK 276 DRLKAYVRDP286 YALDLIDKLL296 VLDPAQRIDD307 DALNHDFFWS317 DPMPSDLKG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TOJ or .TOJ2 or .TOJ3 or :3TOJ;style chemicals stick;color identity;select .A:25 or .A:30 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:153 or .A:154 or .A:156 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: CID 137333456 | Ligand Info | |||||
| Structure Description | Crystal Structure of Human CDK9/cyclinT1 in complex with MC180295 | PDB:6W9E | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | Yes | [8] |
| PDB Sequence |
SVECPFCDEV
16 SKYEKLAKIG26 QGTFGEVFKA36 RHRKTGQKVA46 LKKVLMENEK56 EGFPITALRE 66 IKILQLLKHE76 NVVNLIEICR86 TKASKGSIYL101 VFDFCEHDLA111 GLLSNVLVKF 121 TLSEIKRVMQ131 MLLNGLYYIH141 RNKILHRDMK151 AANVLITRDG161 VLKLADFGLA 171 RAFSLQPNRY185 NRVVTLWYRP196 PELLLGERDY206 GPPIDLWGAG216 CIMAEMWTRS 226 PIMQGNTEQH236 QLALISQLCG246 SITPEVWPNV256 DNYELYEKLE266 LVKGQKRKVK 276 DRLKAYVRDP286 YALDLIDKLL296 VLDPAQRIDD307 DALNHDFFWS317 DPMPSDLKG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TO7 or .TO72 or .TO73 or :3TO7;style chemicals stick;color identity;select .A:25 or .A:30 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:153 or .A:154 or .A:156 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Casein Kinase inhibitor A86 | Ligand Info | |||||
| Structure Description | Crystal Structure of Human CDK9/cyclinT1 with A86 | PDB:6GZH | ||||
| Method | X-ray diffraction | Resolution | 3.17 Å | Mutation | Yes | [13] |
| PDB Sequence |
VECPFCDEVS
17 KYEKLAKIGQ27 GTFGEVFKAR37 HRKTGQKVAL47 KKVLMENEKE57 GFPITALREI 67 KILQLLKHEN77 VVNLIEICRT87 KASGSIYLVF103 DFCEHDLAGL113 LSNVLVKFTL 123 SEIKRVMQML133 LNGLYYIHRN143 KILHRDMKAA153 NVLITRDGVL163 KLADFGLARA 173 FSLAQPNRYN187 RVVTLWYRPP197 ELLLGERDYG207 PPIDLWGAGC217 IMAEMWTRSP 227 IMQGNTEQHQ237 LALISQLCGS247 ITPEVWPNVD257 NYELYEKLEL267 VKGQKRKVKD 277 RLKAYVRDPY287 ALDLIDKLLV297 LDPAQRIDSD307 DALNHDFFWS317 DPMPSDLKG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LCI or .LCI2 or .LCI3 or :3LCI;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:30 or .A:33 or .A:46 or .A:48 or .A:79 or .A:103 or .A:104 or .A:105 or .A:106 or .A:107 or .A:108 or .A:109 or .A:156 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat. Elife. 2013 Mar 5;2:e00327. | ||||
| REF 2 | AFF4 binding to Tat-P-TEFb indirectly stimulates TAR recognition of super elongation complexes at the HIV promoter. Elife. 2014 Apr 24;3:e02375. | ||||
| REF 3 | The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation. EMBO J. 2008 Jul 9;27(13):1907-18. | ||||
| REF 4 | Discovery of AZD4573, a Potent and Selective Inhibitor of CDK9 That Enables Short Duration of Target Engagement for the Treatment of Hematological Malignancies. J Med Chem. 2020 Dec 24;63(24):15564-15590. | ||||
| REF 5 | Crystal structure of HIV-1 Tat complexed with human P-TEFb. Nature. 2010 Jun 10;465(7299):747-51. | ||||
| REF 6 | Halogen bonds form the basis for selective P-TEFb inhibition by DRB. Chem Biol. 2010 Sep 24;17(9):931-6. | ||||
| REF 7 | Comparative structural and functional studies of 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile CDK9 inhibitors suggest the basis for isotype selectivity. J Med Chem. 2013 Feb 14;56(3):660-70. | ||||
| REF 8 | Comparative Modeling of CDK9 Inhibitors to Explore Selectivity and Structure-Activity Relationships | ||||
| REF 9 | The CDK9 C-helix exhibits conformational plasticity that may explain the selectivity of CAN508. ACS Chem Biol. 2012 May 18;7(5):811-6. | ||||
| REF 10 | CDK Inhibitors Roscovitine and CR8 Trigger Mcl-1 Down-Regulation and Apoptotic Cell Death in Neuroblastoma Cells. Genes Cancer. 2010 Apr;1(4):369-80. | ||||
| REF 11 | Substituted 4-(thiazol-5-yl)-2-(phenylamino)pyrimidines are highly active CDK9 inhibitors: synthesis, X-ray crystal structures, structure-activity relationship, and anticancer activities. J Med Chem. 2013 Feb 14;56(3):640-59. | ||||
| REF 12 | Discovery of a Series of 7-Azaindoles as Potent and Highly Selective CDK9 Inhibitors for Transient Target Engagement. J Med Chem. 2021 Oct 28;64(20):15189-15213. | ||||
| REF 13 | Small Molecules Co-targeting CKIAlpha and the Transcriptional Kinases CDK7/9 Control AML in Preclinical Models. Cell. 2018 Sep 20;175(1):171-185.e25. | ||||
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