MolNFT v1 · #146714 · protein
Mapping the binding trajectory of a suicide inhibitor in human indoleamine 2,3-dioxygenase 1
6DPR: “Mapping the binding trajectory of a suicide inhibitor in human indoleamine 2,3-dioxygenase 1”. X-ray diffraction, 2 ligands (H7P, HEM), 5 pockets (best druggability 0.82). MolNFT v1 #146714 on GenesisL1: 3D structure, binding sites…
- PDB
- 6DPR
- Type
- protein
- Length
- 729 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
- H7P, HEM
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 358 | 60% helix, 2% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 371 | 57% helix, 3% strand | P14902 |
Ligands and binding sites
- H7P · (2R)-N-(4-chlorophenyl)-2-[cis-4-(6-fluoroquinolin-4-yl)cyclohexyl]propanamide · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.82 | 0.85 | 66 | H7P |
| 2 | 892 | 0.79 | 0.82 | 95 | EDO |
| 3 | 687 | 0.79 | 0.83 | 45 | HEM, H7P |
| 4 | 732 | 0.77 | 0.81 | 78 | EDO |
| 5 | 67 | 0.31 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 702 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6DPR · Mapping the binding trajectory of a suicide inhibitor in human indoleamine… · 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 6DPR · PDBe 6DPR · UniProt P14902
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