MolNFT v1 · #168005 · protein
CPS1 bound to allosteric inhibitor H3B-374
6W2J · Carbamoyl-phosphate synthase [ammonia], mitochondrial: “CPS1 bound to allosteric inhibitor H3B-374”. X-ray diffraction, 2 ligands (374, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #168005 on GenesisL1: 3D structure, binding…
- PDB
- 6W2J
- Type
- protein
- Length
- 2,786 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbamoyl-phosphate synthase [ammonia], mitochondrial
- EC
- 6.3.4.16
- UniProt
- P31327
- Ligands
- 374, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16) | protein | 1422 | 33% helix, 24% strand | P31327 |
| B | Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16) | protein | 1364 | 32% helix, 24% strand | P31327 |
Ligands and binding sites
- 374 · (2-fluoranyl-4-methoxy-phenyl)-[(3~{R},5~{R})-4-(2-fluoranyl-4-methoxy-phenyl)carbonyl-3,5-dimethyl-piperazin-1-yl]methanone · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.84 | 0.88 | 80 | empty |
| 2 | 1200 | 0.84 | 0.85 | 118 | empty |
| 3 | 258 | 0.82 | 0.94 | 40 | empty |
| 4 | 284 | 0.82 | 0.93 | 40 | empty |
| 5 | 1162 | 0.82 | 0.83 | 116 | empty |
Interfaces
1 interface between chains.
- A–B · 476 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 P31327
- Elsewhere: RCSB PDB 6W2J · PDBe 6W2J · UniProt P31327
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