MolNFT v1 · #126023 · protein
CDK1/CYCLINB1/CKS2 in complex with NU6102
5LQF · Cyclin-dependent kinase 1: “CDK1/CYCLINB1/CKS2 in complex with NU6102”. X-ray diffraction, 1 ligand (4SP), 18 pockets (best druggability 0.84). MolNFT v1 #126023 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LQF
- Type
- protein
- Length
- 1,248 residues
- Chains
- 6
- 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
- 4SP
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 1 (EC 2.7.11.22, 2.7.11.23) | protein | 287 | 36% helix, 18% strand | P06493 |
| B, E | G2/MITOTIC-specific cyclin-B1 | protein | 264 | 68% helix, 0% strand | P14635 |
| C, F | Cyclin-dependent kinases regulatory subunit 2 | protein | 74 | 14% helix, 31% strand | P33552 |
| D | Cyclin-dependent kinase 1 (EC 2.7.11.22, 2.7.11.23) | protein | 285 | 35% helix, 18% strand | P06493 |
Ligands and binding sites
- 4SP · O6-cyclohexylmethoxy-2-(4'-sulphamoylanilino) purine · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.84 | 0.85 | 104 | empty |
| 2 | 165 | 0.79 | 0.95 | 30 | empty |
| 3 | 459 | 0.73 | 0.83 | 59 | 4SP |
| 4 | 314 | 0.71 | 0.84 | 34 | 4SP |
| 5 | 263 | 0.65 | 0.82 | 40 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1546 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1447 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 758 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 740 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 530 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5LQF · CDK1/CyclinB1/CKS2 in complex with NU6102 · the same entry in another collection · chain F against F, 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 E 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 F 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 D 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 5LQF · PDBe 5LQF · UniProt P06493 · UniProt P14635 · UniProt P33552
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