MolNFT v1 · #17177 · protein
Cyclin a binding groove inhibitor ac-arg-arg-leu-asn-(M-cl-phe)-NH2
1OKW · Cell division protein kinase 2: “Cyclin a binding groove inhibitor ac-arg-arg-leu-asn-(M-cl-phe)-NH2”. X-ray diffraction, 2 ligands (ACE, NH2), 17 pockets (best druggability 0.81). MolNFT v1 #17177 on GenesisL1: 3D structure…
- PDB
- 1OKW
- Type
- protein
- Length
- 1,118 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2; ACE-arg-arg-leu-asn-fcl-NH2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- ACE, NH2
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 296 | 33% helix, 16% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 64% helix, 0% strand | P20248 |
| E, F | ACE-arg-arg-leu-asn-fcl-NH2 | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, E, D, F
- 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
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.81 | 0.98 | 22 | empty |
| 2 | 138 | 0.81 | 0.98 | 22 | empty |
| 3 | 735 | 0.75 | 0.80 | 83 | empty |
| 4 | 537 | 0.67 | 0.78 | 57 | empty |
| 5 | 227 | 0.66 | 0.84 | 29 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1771 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1742 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 489 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 481 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 436 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 1OKW · Cyclin A binding groove inhibitor Ac-Arg-Arg-Leu-Asn-(m-Cl-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 1OKW · PDBe 1OKW · UniProt P24941 · UniProt P20248
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.