MolNFT v1 · #168550 · protein
Human IDO1 in complex with compound 4-a
6WJY · Indoleamine 2,3-dioxygenase 1: “Human IDO1 in complex with compound 4-a”. X-ray diffraction, 1 ligand (U41), 8 pockets (best druggability 0.80). MolNFT v1 #168550 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WJY
- Type
- protein
- Length
- 750 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
- U41
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 375 | 62% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 375 | 63% helix, 4% strand | P14902 |
Ligands and binding sites
- U41 · 3-chloro-N-(3-{(2S)-1-[(4-fluorophenyl)amino]-1-oxopropan-2-yl}bicyclo[1.1.1]pentan-1-yl)benzamide · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.80 | 0.84 | 64 | U41 |
| 2 | 672 | 0.80 | 0.84 | 66 | U41 |
| 3 | 710 | 0.76 | 0.81 | 81 | empty |
| 4 | 667 | 0.75 | 0.81 | 69 | empty |
| 5 | 63 | 0.69 | 0.96 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6WJY · Human IDO1 in complex with compound 4-a · 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 6WJY · PDBe 6WJY · UniProt P14902
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