Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T70176 | Target Info | |||
| Target Name | Cyclin-dependent kinase 2 (CDK2) | ||||
| Synonyms | Sin3 associated polypeptide; SIN3-associated protein; P33 protein kinase; Cell division protein kinase 2; CDKN2 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | CDK2 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | NU-6102 | Ligand Info | |||
| Canonical SMILES | C1CCC(CC1)COC2=NC(=NC3=C2NC=N3)NC4=CC=C(C=C4)S(=O)(=O)N | ||||
| InChI | 1S/C18H22N6O3S/c19-28(25,26)14-8-6-13(7-9-14)22-18-23-16-15(20-11-21-16)17(24-18)27-10-12-4-2-1-3-5-12/h6-9,11-12H,1-5,10H2,(H2,19,25,26)(H2,20,21,22,23,24) | ||||
| InChIKey | OWXORKPNCHJYOF-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 4566 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 2C6O Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [1] |
| PDB Sequence |
MENFQKVEKI
10 GEGTYGVVYK20 ARNKLTGEVV30 ALKKIRLVPS46 TAIREISLLK56 ELNHPNIVKL 66 LDVIHTENKL76 YLVFEFLHQD86 LKKFMDASAL96 TGIPLPLIKS106 YLFQLLQGLA 116 FCHSHRVLHR126 DLKPQNLLIN136 TEGAIKLADF146 GLARAFGVPV156 RTYTHEVVTL 166 WYRAPEILLG176 CKYYSTAVDI186 WSLGCIFAEM196 VTRRALFPGD206 SEIDQLFRIF 216 RTLGTPDEVV226 WPGVTSMPDY236 KPSFPKWARQ246 DFSKVVPPLD256 EDGRSLLSQM 266 LHYDPNKRIS276 AKAALAHPFF286 QDVTKPVPHL296
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ILE10
3.389
GLY11
4.343
GLU12
4.645
GLY13
3.518
THR14
4.889
VAL18
3.412
ALA31
3.367
LYS33
3.074
VAL64
3.928
PHE80
3.598
GLU81
2.962
PHE82
3.611
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| PDB ID: 4EOR Thr 160 phosphorylated CDK2 WT - human cyclin A3 complex with the inhibitor NU6102 | ||||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [2] |
| PDB Sequence |
SMENFQKVEK
9 IGEGTYGVVY19 KARNKLTGEV29 VALKKIRLEG43 VPSTAIREIS53 LLKELNHPNI 63 VKLLDVIHTE73 NKLYLVFEFL83 HQDLKKFMDA93 SALTGIPLPL103 IKSYLFQLLQ 113 GLAFCHSHRV123 LHRDLKPQNL133 LINTEGAIKL143 ADFGLARAFG153 VPVRTYHEVV 164 TLWYRAPEIL174 LGCKYYSTAV184 DIWSLGCIFA194 EMVTRRALFP204 GDSEIDQLFR 214 IFRTLGTPDE224 VVWPGVTSMP234 DYKPSFPKWA244 RQDFSKVVPP254 LDEDGRSLLS 264 QMLHYDPNKR274 ISAKAALAHP284 FFQDVTKPVP294 HLR
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| PDB ID: 4EOK Thr 160 phosphorylated CDK2 H84S, Q85M, K89D - human cyclin A3 complex with the inhibitor NU6102 | ||||||
| Method | X-ray diffraction | Resolution | 2.57 Å | Mutation | Yes | [2] |
| PDB Sequence |
SMENFQKVEK
9 IGEGTYGVVY19 KARNKLTGEV29 VALKKIRLEG43 VPSTAIREIS53 LLKELNHPNI 63 VKLLDVIHTE73 NKLYLVFEFL83 SMDLKDFMDA93 SALTGIPLPL103 IKSYLFQLLQ 113 GLAFCHSHRV123 LHRDLKPQNL133 LINTEGAIKL143 ADFGLARAFG153 VPVRTYHEVV 164 TLWYRAPEIL174 LGCKYYSTAV184 DIWSLGCIFA194 EMVTRRALFP204 GDSEIDQLFR 214 IFRTLGTPDE224 VVWPGVTSMP234 DYKPSFPKWA244 RQDFSKVVPP254 LDEDGRSLLS 264 QMLHYDPNKR274 ISAKAALAHP284 FFQDVTKPVP294 HLR
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| PDB ID: 2IW9 STRUCTURE OF HUMAN THR160-PHOSPHO CDK2-CYCLIN A COMPLEXED WITH A BISANILINOPYRIMIDINE INHIBITOR | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [3] |
| PDB Sequence |
SMENFQKVEK
9 IGEGTYGVVY19 KARNKLTGEV29 VALKKIRLEG43 VPSTAIREIS53 LLKELNHPNI 63 VKLLDVIHTE73 NKLYLVFEFL83 HQDLKTFMDA93 SALTGIPLPL103 IKSYLFQLLQ 113 GLAFCHSHRV123 LHRDLKPQNL133 LINTEGAIKL143 ADFGLARAFG153 VPVRTYHEVV 164 TLWYRAPEIL174 LGCKYYSTAV184 DIWSLGCIFA194 EMVTRRALFP204 GDSEIDQLFR 214 IFRTLGTPDE224 VVWPGVTSMP234 DYKPSFPKWA244 RQDFSKVVPP254 LDEDGRSLLS 264 QMLHYDPNKR274 ISAKAALAHP284 FFQDVTKPVP294 HLR
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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 .4SP or .4SP2 or .4SP3 or :34SP;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: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:131 or .A:132 or .A:134 or .A:144 or .A:145; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 2IW8 STRUCTURE OF HUMAN THR160-PHOSPHO CDK2-CYCLIN A F82H-L83V-H84D MUTANT WITH AN O6-CYCLOHEXYLMETHYLGUANINE INHIBITOR | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | Yes | [3] |
| PDB Sequence |
SMENFQKVEK
9 IGEGTYGVVY19 KARNKLTGEV29 VALKKIRLDT39 ETEGVPSTAI49 REISLLKELN 59 HPNIVKLLDV69 IHTENKLYLV79 FEHVDQDLKK89 FMDASALTGI99 PLPLIKSYLF 109 QLLQGLAFCH119 SHRVLHRDLK129 PQNLLINTEG139 AIKLADFGLA149 RAFGVPVRTY 159 HEVVTLWYRA170 PEILLGCKYY180 STAVDIWSLG190 CIFAEMVTRR200 ALFPGDSEID 210 QLFRIFRTLG220 TPDEVVWPGV230 TSMPDYKPSF240 PKWARQDFSK250 VVPPLDEDGR 260 SLLSQMLHYD270 PNKRISAKAA280 LAHPFFQDVT290 KPVPHLR
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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 .4SP or .4SP2 or .4SP3 or :34SP;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: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:131 or .A:132 or .A:134 or .A:144 or .A:145; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 1H1S Structure of human Thr160-phospho CDK2/cyclin A complexed with the inhibitor NU6102 | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [4] |
| PDB Sequence |
SMENFQKVEK
9 IGEGTYGVVY19 KARNKLTGEV29 VALKKIRLDT39 ETEGVPSTAI49 REISLLKELN 59 HPNIVKLLDV69 IHTENKLYLV79 FEFLHQDLKK89 FMDASALTGI99 PLPLIKSYLF 109 QLLQGLAFCH119 SHRVLHRDLK129 PQNLLINTEG139 AIKLADFGLA149 RAFGVPVRTY 159 HEVVTLWYRA170 PEILLGCKYY180 STAVDIWSLG190 CIFAEMVTRR200 ALFPGDSEID 210 QLFRIFRTLG220 TPDEVVWPGV230 TSMPDYKPSF240 PKWARQDFSK250 VVPPLDEDGR 260 SLLSQMLHYD270 PNKRISAKAA280 LAHPFFQDVT290 KPVPHL
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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 .4SP or .4SP2 or .4SP3 or :34SP;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: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:131 or .A:132 or .A:134 or .A:144 or .A:145; 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 | Triazolo[1,5-a]pyrimidines as novel CDK2 inhibitors: protein structure-guided design and SAR. Bioorg Med Chem Lett. 2006 Mar 1;16(5):1353-7. | ||||
| REF 2 | An integrated chemical biology approach provides insight into Cdk2 functional redundancy and inhibitor sensitivity. Chem Biol. 2012 Aug 24;19(8):1028-40. | ||||
| REF 3 | Dissecting the determinants of cyclin-dependent kinase 2 and cyclin-dependent kinase 4 inhibitor selectivity. J Med Chem. 2006 Sep 7;49(18):5470-7. | ||||
| REF 4 | Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor. Nat Struct Biol. 2002 Oct;9(10):745-9. | ||||
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