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 | 3-(1H-imidazol-5-ylmethylidene)-5-methoxy-1H-indol-2-one | Ligand Info | |||
| Canonical SMILES | COC1=CC2=C(C=C1)NC(=O)C2=CC3=CN=CN3 | ||||
| InChI | 1S/C13H11N3O2/c1-18-9-2-3-12-10(5-9)11(13(17)16-12)4-8-6-14-7-15-8/h2-7H,1H3,(H,14,15)(H,16,17) | ||||
| InChIKey | QNUKRWAIZMBVCU-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 24906268 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1PF8 Crystal Structure of Human Cyclin-Dependent Kinase 2 Complexed with a Nucleoside Inhibitor | ||||||
| Method | X-ray diffraction | Resolution | 2.51 Å | Mutation | No | [1] |
| PDB Sequence |
MENFQKVEKI
10 GEGTYGVVYK20 ARNKLTGEVV30 ALKKIRLDTE40 TEGVPSTAIR50 EISLLKELNH 60 PNIVKLLDVI70 HTENKLYLVF80 EFLHQDLKKF90 MDASALTGIP100 LPLIKSYLFQ 110 LLQGLAFCHS120 HRVLHRDLKP130 QNLLINTEGA140 IKLADFGLAR150 AFGVPVRTYT 160 HEVVTLWYRA170 PEILLGCKYY180 STAVDIWSLG190 CIFAEMVTRR200 ALFPGDSEID 210 QLFRIFRTLG220 TPDEVVWPGV230 TSMPDYKPSF240 PKWARQDFSK250 VVPPLDEDGR 260 SLLSQMLHYD270 PNKRISAKAA280 LAHPFFQDVT290 KPVPHLRL
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| PDB ID: 6GUC CDK2/CyclinA in complex with SU9516 | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [2] |
| PDB Sequence |
SMENFQKVEK
9 IGEGTYGVVY19 KARNKLTGEV29 VALKKITEGV44 PSTAIREISL54 LKELNHPNIV 64 KLLDVIHTEN74 KLYLVFEFLH84 QDLKKFMDAS94 ALTGIPLPLI104 KSYLFQLLQG 114 LAFCHSHRVL124 HRDLKPQNLL134 INTEGAIKLA144 DFGLARAFGV154 PVRTYHEVVT 165 LWYRAPEILL175 GCKYYSTAVD185 IWSLGCIFAE195 MVTRRALFPG205 DSEIDQLFRI 215 FRTLGTPDEV225 VWPGVTSMPD235 YKPSFPKWAR245 QDFSKVVPPL255 DEDGRSLLSQ 265 MLHYDPNKRI275 SAKAALAHPF285 FQDVTKPVPH295 L
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| PDB ID: 3PY0 CDK2 in complex with inhibitor SU9516 | ||||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [3] |
| PDB Sequence |
MENFQKVEKI
10 GEGTYGVVYK20 ARNKLTGEVV30 ALKKIRTEGV44 PSTAIREISL54 LKELNHPNIV 64 KLLDVIHTEN74 KLYLVFEFLH84 QDLKKFMDAS94 ALTGIPLPLI104 KSYLFQLLQG 114 LAFCHSHRVL124 HRDLKPQNLL134 INTEGAIKLA144 DFGLARAFGV154 PVRTYTHEVV 164 TLWYRAPEIL174 LGCKYYSTAV184 DIWSLGCIFA194 EMVTRRALFP204 GDSEIDQLFR 214 IFRTLGTPDE224 VVWPGVTSMP234 DYKPSFPKWA244 RQDFSKVVPP254 LDEDGRSLLS 264 QMLHYDPNKR274 ISAKAALAHP284 FFQDVTKPVP294 HLRL
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| PDB ID: 3PY1 CDK2 ternary complex with SU9516 and ANS | ||||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [3] |
| PDB Sequence |
SPEFMENFQK
6 VEKIGEGTYG16 VVYKARNKLT26 GEVVALKKIR36 LDTETEGVPS46 TAIREISLLK 56 ELNHPNIVKL66 LDVIHTENKL76 YLVFEFLHQD86 LKKFMDASAL96 TGIPLPLIKS 106 YLFQLLQGLA116 FCHSHRVLHR126 DLKPQNLLIN136 TEGAIKLADF146 GLARAFGVPV 156 RTYTHEVVTL166 WYRAPEILLG176 CKYYSTAVDI186 WSLGCIFAEM196 VTRRALFPGD 206 SEIDQLFRIF216 RTLGTPDEVV226 WPGVTSMPDY236 KPSFPKWARQ246 DFSKVVPPLD 256 EDGRSLLSQM266 LHYDPNKRIS276 AKAALAHPFF286 QDVTKPVPHL296 RL |
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | SU9516: biochemical analysis of cdk inhibition and crystal structure in complex with cdk2. Biochem Biophys Res Commun. 2003 Oct 24;310(3):1026-31. | ||||
| REF 2 | 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 3 | Discovery of a potential allosteric ligand binding site in CDK2. ACS Chem Biol. 2011 May 20;6(5):492-501. | ||||
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