MolNFT v1 · #150452 · protein
CDK1/CYCLINB/CKS2 in complex with flavopiridol
6GU2 · Cyclin-dependent kinase 1: “CDK1/CYCLINB/CKS2 in complex with flavopiridol”. X-ray diffraction, 1 ligand (F9Z), 9 pockets (best druggability 0.81). MolNFT v1 #150452 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GU2
- Type
- protein
- Length
- 631 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
- F9Z
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 1 (EC 2.7.11.22, 2.7.11.23) | protein | 294 | 35% helix, 19% strand | P06493 |
| B | G2/MITOTIC-specific cyclin-B1 | protein | 265 | 68% helix, 0% strand | P14635 |
| C | Cyclin-dependent kinases regulatory subunit 2 | protein | 72 | 14% helix, 31% strand | P33552 |
Ligands and binding sites
- F9Z · 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.81 | 0.96 | 26 | empty |
| 2 | 517 | 0.69 | 0.79 | 56 | F9Z |
| 3 | 114 | 0.59 | 0.85 | 19 | empty |
| 4 | 194 | 0.52 | 0.78 | 35 | empty |
| 5 | 93 | 0.50 | 0.82 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1396 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 744 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6GU2 · CDK1/CyclinB/Cks2 in complex with Flavopiridol · 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 0.98
- 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 0.90
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 6GU2 · PDBe 6GU2 · UniProt P06493 · UniProt P14635 · UniProt P33552
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