MolNFT v1 · #17176 · protein
Cyclin a binding groove inhibitor H-arg-arg-leu-ile-phe-NH2
1OKV · Cell division protein kinase 2: “Cyclin a binding groove inhibitor H-arg-arg-leu-ile-phe-NH2”. X-ray diffraction, 1 ligand (NH2), 13 pockets (best druggability 0.80). MolNFT v1 #17176 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1OKV
- Type
- protein
- Length
- 1,119 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2; H-arg-arg-leu-ile-phe-NH2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- NH2
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 295 | 34% helix, 15% strand | P24941 |
| B | Cyclin A2 | protein | 258 | 64% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 296 | 33% helix, 17% strand | P24941 |
| D | Cyclin A2 | protein | 260 | 64% helix, 0% strand | P20248 |
| E, F | H-arg-arg-leu-ile-phe-NH2 | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 2 copies · chains B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.80 | 0.98 | 21 | empty |
| 2 | 129 | 0.80 | 0.97 | 24 | empty |
| 3 | 945 | 0.78 | 0.80 | 103 | empty |
| 4 | 503 | 0.66 | 0.77 | 57 | empty |
| 5 | 220 | 0.66 | 0.84 | 31 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1771 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1730 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 515 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 497 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 435 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1OKV · Cyclin A binding groove inhibitor H-Arg-Arg-Leu-Ile-Phe-NH2 · the same entry in another collection · chain F against F, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 P24941
- Every structure of UniProt P20248
- Elsewhere: RCSB PDB 1OKV · PDBe 1OKV · UniProt P24941 · UniProt P20248
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