MolNFT v1 · #24310 · protein
Cyclin a binding groove inhibitor ACE-arg-lys-leu-phe-gly
1URC · Cell division protein kinase 2: “Cyclin a binding groove inhibitor ACE-arg-lys-leu-phe-gly”. X-ray diffraction, 1 ligand (ACE), 15 pockets (best druggability 0.81). MolNFT v1 #24310 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1URC
- 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; Peptide inhibitor
- EC
- 2.7.1.37, 2.7.11.22
- UniProt
- P24941, P20248
- Ligands
- ACE
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.37, 2.7.11.22) | protein | 296 | 33% helix, 18% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 67% helix, 0% strand | P20248 |
| E, F | Peptide inhibitor | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.81 | 0.98 | 22 | empty |
| 2 | 129 | 0.80 | 0.98 | 23 | empty |
| 3 | 960 | 0.77 | 0.79 | 100 | empty |
| 4 | 209 | 0.69 | 0.86 | 29 | empty |
| 5 | 200 | 0.67 | 0.85 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1734 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1653 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 499 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 483 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 405 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 isopeptide (covalent ligand, isopeptide).
Compared structures
- 1URC · Cyclin A binding groove inhibitor Ace-Arg-Lys-Leu-Phe-Gly · 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 1.00
- 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 1URC · PDBe 1URC · UniProt P24941 · UniProt P20248
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