MolNFT v1 · #110782 · protein
Human CDK1/CYCLINB1/CKS2 with inhibitor
4Y72 · Cyclin-dependent kinase 1: “Human CDK1/CYCLINB1/CKS2 with inhibitor”. X-ray diffraction, 1 ligand (LZ9), 11 pockets (best druggability 0.81). MolNFT v1 #110782 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Y72
- Type
- protein
- Length
- 630 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 1; G2/MITOTIC-specific cyclin-B1; Cyclin-dependent kinases…
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P06493, P14635, P33552
- Ligands
- LZ9
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 1 (EC 2.7.11.22, 2.7.11.23) | protein | 292 | 34% helix, 18% strand | P06493 |
| B | G2/MITOTIC-specific cyclin-B1 | protein | 264 | 68% helix, 0% strand | P14635 |
| C | Cyclin-dependent kinases regulatory subunit 2 | protein | 74 | 15% helix, 30% strand | P33552 |
Ligands and binding sites
- LZ9 · {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.81 | 0.96 | 26 | empty |
| 2 | 494 | 0.72 | 0.81 | 64 | LZ9 |
| 3 | 344 | 0.59 | 0.76 | 39 | empty |
| 4 | 98 | 0.47 | 0.80 | 17 | empty |
| 5 | 83 | 0.41 | 0.79 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1352 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 749 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4Y72 · Human CDK1/CyclinB1/CKS2 With Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P14635 · AlphaFold monomer V2.0 prediction for G2/MITOTIC-specific cyclin-B1 (P14635) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P33552 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinases regulatory subunit 2… · a predicted model of the same protein · chain C against A, TM-score 0.94
- P06493 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 1 (P06493) · a predicted model of the same protein · chain A against A, TM-score 0.93
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P06493
- Every structure of UniProt P14635
- Every structure of UniProt P33552
- Elsewhere: RCSB PDB 4Y72 · PDBe 4Y72 · UniProt P06493 · UniProt P14635 · UniProt P33552
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