MolNFT v1 · #143445 · protein
IDO1/BMS-978587 crystal structure
6AZV · Indoleamine 2,3-dioxygenase 1: “IDO1/BMS-978587 crystal structure”. X-ray diffraction, 1 ligand (C4V), 19 pockets (best druggability 0.88). MolNFT v1 #143445 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AZV
- Type
- protein
- Length
- 1,462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Indoleamine 2,3-dioxygenase 1
- EC
- 1.13.11.52
- UniProt
- P14902
- Ligands
- C4V
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 367 | 60% helix, 3% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 367 | 62% helix, 4% strand | P14902 |
| C | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 362 | 60% helix, 4% strand | P14902 |
| D | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 366 | 60% helix, 4% strand | P14902 |
Ligands and binding sites
- C4V · (1R,2S)-2-(4-[bis(2-methylpropyl)amino]-3-{[(4-methylphenyl)carbamoyl]amino}phenyl)cyclopropane-1-carboxylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.88 | 0.89 | 100 | C4V |
| 2 | 604 | 0.81 | 0.86 | 57 | C4V |
| 3 | 629 | 0.81 | 0.86 | 58 | C4V |
| 4 | 650 | 0.81 | 0.85 | 63 | C4V |
| 5 | 737 | 0.75 | 0.80 | 74 | empty |
Interfaces
4 interfaces between chains.
- A–B · 789 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 625 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 272 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 169 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
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 P14902
- Elsewhere: RCSB PDB 6AZV · PDBe 6AZV · UniProt P14902
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