Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T49898 | Target Info | |||
| Target Name | Cyclin-dependent kinase 1 (CDK1) | ||||
| Synonyms | P34CDC2; P34 protein kinase; CDKN1; CDC28A; CDC2 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | CDK1 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: AZD-5438 | Ligand Info | |||||
| Structure Description | CDK1/CyclinB/Cks2 in complex with AZD5438 | PDB:6GU3 | ||||
| Method | X-ray diffraction | Resolution | 2.65 Å | Mutation | Yes | [1] |
| PDB Sequence |
LGSMEDYTKI
7 EKIGEGTYGV17 VYKGRHKTTG27 QVVAMKKIRL37 ESEEEGVPST47 AIREISLLKE 57 LRHPNIVSLQ67 DVLMQDSRLY77 LIFEFLSMDL87 KKYLDSIPPG97 QYMDSSLVKS 107 YLYQILQGIV117 FCHSRRVLHR127 DLKPQNLLID137 DKGTIKLADF147 GLARAFGIPI 157 RVYTHEVVTL167 WYRSPEVLLG177 SARYSTPVDI187 WSIGTIFAEL197 ATKKPLFHGD 207 SEIDQLFRIF217 RALGTPNNEV227 WPEVESLQDY237 KNTFPKWKPG247 SLASHVKNLD 257 ENGLDLLSKM267 LIYDPAKRIS277 GKMALNHPYF287 ND
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: NU-6102 | Ligand Info | |||||
| Structure Description | CDK1/CyclinB1/CKS2 in complex with NU6102 | PDB:5LQF | ||||
| Method | X-ray diffraction | Resolution | 2.06 Å | Mutation | No | [2] |
| PDB Sequence |
LGSMEDYTKI
7 EKIGEGTYGV17 VYKGRHKTTG27 QVVAMKKIRL37 ESEEEGVPST47 AIREISLLKE 57 LRHPNIVSLQ67 DVLMQDSRLY77 LIFEFLSMDL87 KKYLDSIPPG97 QYMDSSLVKS 107 YLYQILQGIV117 FCHSRRVLHR127 DLKPQNLLID137 DKGTIKLADF147 GLARAFGIPI 157 RVVTLWYRSP172 EVLLGSARYS182 TPVDIWSIGT192 IFAELATKKP202 LFHGDSEIDQ 212 LFRIFRALGT222 PNNEVWPEVE232 SLQDYKNTFP242 KWKPGSLASH252 VKNLDENGLD 262 LLSKMLIYDP272 AKRISGKMAL282 NHPYFND
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| Ligand Name: CGP74514A | Ligand Info | |||||
| Structure Description | CDK1/CyclinB/Cks2 in complex with CGP74514A | PDB:6GU4 | ||||
| Method | X-ray diffraction | Resolution | 2.73 Å | Mutation | Yes | [1] |
| PDB Sequence |
LGSMEDYTKI
7 EKIGEGTYGV17 VYKGRHKTTG27 QVVAMKKIRL37 ESEEEGVPST47 AIREISLLKE 57 LRHPNIVSLQ67 DVLMQDSRLY77 LIFEFLSMDL87 KKYLDSIPPG97 QYMDSSLVKS 107 YLYQILQGIV117 FCHSRRVLHR127 DLKPQNLLID137 DKGTIKLADF147 GLARAFGIPI 157 RVYTHEVVTL167 WYRSPEVLLG177 SARYSTPVDI187 WSIGTIFAEL197 ATKKPLFHGD 207 SEIDQLFRIF217 RALGTPNNEV227 WPEVESLQDY237 KNTFPKWKPG247 SLASHVKNLD 257 ENGLDLLSKM267 LIYDPAKRIS277 GKMALNHPYF287 ND
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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 .FC8 or .FC82 or .FC83 or :3FC8;style chemicals stick;color identity;select .A:10 or .A:11 or .A:12 or .A:13 or .A:18 or .A:31 or .A:33 or .A:64 or .A:80 or .A:81 or .A:82 or .A:83 or .A:84 or .A:85 or .A:86 or .A:89 or .A:132 or .A:133 or .A:135; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one | Ligand Info | |||||
| Structure Description | CDK1/CyclinB/Cks2 in complex with Flavopiridol | PDB:6GU2 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [1] |
| PDB Sequence |
LGSMEDYTKI
7 EKIGEGTYGV17 VYKGRHKTTG27 QVVAMKKIRL37 ESEEEGVPST47 AIREISLLKE 57 LRHPNIVSLQ67 DVLMQDSRLY77 LIFEFLSMDL87 KKYLDSIPPG97 QYMDSSLVKS 107 YLYQILQGIV117 FCHSRRVLHR127 DLKPQNLLID137 DKGTIKLADF147 GLARAFGIPI 157 RVYTVTLWYR170 SPEVLLGSAR180 YSTPVDIWSI190 GTIFAELATK200 KPLFHGDSEI 210 DQLFRIFRAL220 GTPNNEVWPE230 VESLQDYKNT240 FPKWKPGSLA250 SHVKNLDENG 260 LDLLSKMLIY270 DPAKRISGKM280 ALNHPYFNDL290 DNQI
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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 .F9Z or .F9Z2 or .F9Z3 or :3F9Z;style chemicals stick;color identity;select .A:10 or .A:11 or .A:15 or .A:18 or .A:31 or .A:33 or .A:64 or .A:80 or .A:81 or .A:82 or .A:83 or .A:84 or .A:85 or .A:86 or .A:132 or .A:133 or .A:135 or .A:145 or .A:146; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide | Ligand Info | |||||
| Structure Description | Human CDK1/CyclinB1/CKS2 With Inhibitor | PDB:4Y72 | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [3] |
| PDB Sequence |
LGSMEDYTKI
7 EKIGEGTYGV17 VYKGRHKTTG27 QVVAMKKIRL37 ESEEEGVPST47 AIREISLLKE 57 LRHPNIVSLQ67 DVLMQDSRLY77 LIFEFLSMDL87 KKYLDSIPPG97 QYMDSSLVKS 107 YLYQILQGIV117 FCHSRRVLHR127 DLKPQNLLID137 DKGTIKLADF147 GLARAFGIPI 157 RVYTHEVVTL167 WYRSPEVLLG177 SARYSTPVDI187 WSIGTIFAEL197 ATKKPLFHGD 207 SEIDQLFRIF217 RALGTPNNEV227 WPEVESLQDY237 KNTFPKWKPG247 SLASHVKNLD 257 ENGLDLLSKM267 LIYDPAKRIS277 GKMALNHPYF287 ND
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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 .LZ9 or .LZ92 or .LZ93 or :3LZ9;style chemicals stick;color identity;select .A:10 or .A:15 or .A:18 or .A:31 or .A:33 or .A:64 or .A:80 or .A:81 or .A:82 or .A:83 or .A:84 or .A:85 or .A:86 or .A:89 or .A:132 or .A:133 or .A:135 or .A:145 or .A:146; 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: 3-[({3-Ethyl-5-[(2s)-2-(2-Hydroxyethyl)piperidin-1-Yl]pyrazolo[1,5-A]pyrimidin-7-Yl}amino)methyl]-1-Hydroxypyridinium | Ligand Info | |||||
| Structure Description | CDK1/Cks2 in complex with Dinaciclib | PDB:6GU6 | ||||
| Method | X-ray diffraction | Resolution | 2.33 Å | Mutation | No | [1] |
| PDB Sequence |
MEDYTKIEKI
10 GEGTYGVVYK20 GRHKTTGQVV30 AMKKIRLESE40 EEGVPSTAIR50 EISLLKELRH 60 PNIVSLQDVL70 MQDSRLYLIF80 EFLSMDLKKY90 LDSIPPGQYM100 DSSLVKSYLY 110 QILQGIVFCH120 SRRVLHRDLK130 PQNLLIDDKG140 TIKLADFGLA150 RAFGIPITHE 163 VVTLWYRSPE173 VLLGSARYST183 PVDIWSIGTI193 FAELATKKPL203 FHGDSEIDQL 213 FRIFRALGTP223 NNEVWPEVES233 LQDYKNTFPK243 WKPGSLASHV253 KNLDENGLDL 263 LSKMLIYDPA273 KRISGKMALN283 HPYFNDLD
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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 .1QK or .1QK2 or .1QK3 or :31QK;style chemicals stick;color identity;select .A:10 or .A:11 or .A:12 or .A:13 or .A:18 or .A:31 or .A:33 or .A:64 or .A:80 or .A:81 or .A:82 or .A:83 or .A:84 or .A:85 or .A:86 or .A:89 or .A:132 or .A:133 or .A:135 or .A:145 or .A:146; 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 | Differences in the Conformational Energy Landscape of CDK1 and CDK2 Suggest a Mechanism for Achieving Selective CDK Inhibition. Cell Chem Biol. 2019 Jan 17;26(1):121-130.e5. | ||||
| REF 2 | Cyclin-Dependent Kinase (CDK) Inhibitors: Structure-Activity Relationships and Insights into the CDK-2 Selectivity of 6-Substituted 2-Arylaminopurines. J Med Chem. 2017 Mar 9;60(5):1746-1767. | ||||
| REF 3 | CDK1 structures reveal conserved and unique features of the essential cell cycle CDK. Nat Commun. 2015 Apr 13;6:6769. | ||||
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