Research workbench
Human IDO1 in complex with compound 17 (N-{2-[(4-{N-[(7S)-4- FLUOROBICYCLO[4.2.0]OCTA-1,3,5-trien-7-yl]-N'-hydroxycarbamimidoyl}- 1,2,5-oxadiazol-3-YL)SULFANYL]ETHYL}ACETAMIDE)
Analyse Human IDO1 in complex with compound 17 (N-{2-[(4-{N-[(7S)-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PU7
- 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, OY4
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 2 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 | 375 | 60% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 374 | 61% helix, 4% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OY4 · N-{2-[(4-{N-[(7S)-4-fluorobicyclo[4.2.0]octa-1,3,5-trien-7-yl]-N'-hydroxycarbamimidoyl}-1,2,5-oxadiazol-3-yl)sulfanyl]ethyl}acetamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.88 | 0.89 | 143 | HEM, OY4 |
| 2 | 623 | 0.80 | 0.85 | 51 | HEM, OY4 |
| 3 | 114 | 0.40 | 0.75 | 23 | empty |
| 4 | 63 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 703 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6PU7 · Human IDO1 in complex with compound 17 (N-{2-[(4-{N-[(7S)-4-fluorobicyclo[4.2.0]octa-1,3,5… · 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 6PU7 · PDBe 6PU7 · UniProt P14902
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