MolNFT v1 · #138389 · protein
Discovery of a novel and selective ido-1 inhibitor pf-06840003 and its characterization as a potential clinical candidate.
5WHR · Indoleamine 2,3-dioxygenase 1: “Discovery of a novel and selective ido-1 inhibitor pf-06840003 and its characterization as a potential…”. X-ray diffraction, 2 ligands (HEM, AOJ), 8 pockets (best druggability 0.90). MolNFT v1 #138389…
- PDB
- 5WHR
- Type
- protein
- Length
- 749 residues
- Chains
- 2
- 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
- HEM, AOJ
- Pockets
- 8 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 375 | 59% helix, 3% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 374 | 59% helix, 3% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- AOJ · (3R)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.90 | 0.92 | 141 | HEM, AOJ |
| 2 | 442 | 0.87 | 0.94 | 45 | HEM, AOJ |
| 3 | 59 | 0.48 | 0.85 | 18 | empty |
| 4 | 111 | 0.45 | 0.78 | 24 | empty |
| 5 | 72 | 0.41 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 694 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5WHR · Discovery of a novel and selective IDO-1 inhibitor PF-06840003 and its characterization… · the same entry in another collection · chain A against A, TM-score 1.00
- P14902 · AlphaFold monomer V2.0 prediction for indoleamine 2,3-dioxygenase 1 (P14902) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 5WHR · PDBe 5WHR · UniProt P14902
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