MolNFT v1 · #103554 · protein
Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with imidazothiazole derivative
4PK6 · Indoleamine 2,3-dioxygenase 1: “Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with imidazothiazole derivative”. X-ray diffraction, 2 ligands (HEM, PKL), 8 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 4PK6
- Type
- protein
- Length
- 746 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, PKL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 373 | 55% helix, 3% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PKL · N-[2-(3-chlorophenyl)ethyl]-3-(4-methylphenyl)imidazo[2,1-b][1,3]thiazole-5-carboxamide · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.85 | 0.87 | 73 | HEM, PKL |
| 2 | 776 | 0.84 | 0.87 | 93 | empty |
| 3 | 845 | 0.84 | 0.86 | 58 | HEM, PKL |
| 4 | 276 | 0.65 | 0.81 | 32 | empty |
| 5 | 64 | 0.38 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 896 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4PK6 · Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with… · 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 A against A, TM-score 0.97
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 4PK6 · PDBe 4PK6 · UniProt P14902
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