Research workbench
Cyclin a binding groove inhibitor H-cit-cit-leu-ile-(P-F-phe)-NH2
Analyse Cyclin a binding groove inhibitor H-cit-cit-leu-ile-(P-F-phe)-NH2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OL1
- Type
- protein
- Length
- 1,114 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2; Cir-cir-leu-ile-pff-NH2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- CIR, NH2
- Pockets
- 16 · best druggability 0.82
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 | 34% helix, 16% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 62% helix, 0% strand | P20248 |
| F, H | Cir-cir-leu-ile-pff-NH2 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · 4 copies · chains B, F, D, H
- NH2 · Amino group · ion · 2 copies · chains B, F, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.82 | 0.98 | 25 | empty |
| 2 | 121 | 0.80 | 0.98 | 22 | empty |
| 3 | 946 | 0.78 | 0.80 | 97 | empty |
| 4 | 227 | 0.70 | 0.86 | 23 | empty |
| 5 | 225 | 0.68 | 0.85 | 22 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1768 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1739 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 540 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 492 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 254 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 1OL1 · Cyclin A binding groove inhibitor H-Cit-Cit-Leu-Ile-(p-F-Phe)-NH2 · the same entry in another collection · chain H against H, 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 0.92
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 1OL1 · PDBe 1OL1 · UniProt P24941 · UniProt P20248
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