MolNFT v1 · #168726 · protein
Human IDO1 in complex with compound 4
6WPE · Indoleamine 2,3-dioxygenase 1: “Human IDO1 in complex with compound 4”. X-ray diffraction, 1 ligand (U6G), 7 pockets (best druggability 0.82). MolNFT v1 #168726 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WPE
- Type
- protein
- Length
- 752 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
- U6G
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 376 | 61% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 376 | 62% helix, 4% strand | P14902 |
Ligands and binding sites
- U6G · 4-chloro-N-{[1-(3-chlorobenzene-1-carbonyl)-1,2,3,4-tetrahydroquinolin-6-yl]methyl}benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.82 | 0.84 | 70 | U6G |
| 2 | 733 | 0.81 | 0.84 | 63 | U6G |
| 3 | 734 | 0.78 | 0.82 | 68 | empty |
| 4 | 775 | 0.78 | 0.82 | 83 | empty |
| 5 | 105 | 0.40 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 801 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6WPE · Human IDO1 in complex with compound 4 · the same entry in another collection · chain A against A, TM-score 1.00
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 6WPE · PDBe 6WPE · UniProt P14902
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