MolNFT v1 · #142441 · protein
Crystal structure of human tdo inhibitor complex
6A4I · Tryptophan 2,3-dioxygenase: “Crystal structure of human tdo inhibitor complex”. X-ray diffraction, 3 ligands (HEM, 9R9, TRP), 20 pockets (best druggability 0.87). MolNFT v1 #142441 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6A4I
- Type
- protein
- Length
- 1,244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan 2,3-dioxygenase
- EC
- 1.13.11.11
- UniProt
- P48775
- Ligands
- HEM, 9R9, TRP
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 322 | 70% helix, 0% strand | P48775 |
| B | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 309 | 70% helix, 0% strand | P48775 |
| C | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 323 | 69% helix, 0% strand | P48775 |
| D | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 290 | 66% helix, 0% strand | P48775 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- 9R9 · 1-(6-chloro-1H-indazol-4-yl)cyclohexan-1-ol · ligand · 4 copies · chains A, B, C, D
- TRP · Tryptophan · ligand · 3 copies · chains A, B, D
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.87 | 0.92 | 90 | empty |
| 2 | 938 | 0.78 | 0.80 | 78 | HEM, 9R9 |
| 3 | 393 | 0.77 | 0.86 | 37 | HEM, 9R9 |
| 4 | 950 | 0.77 | 0.79 | 85 | HEM, 9R9 |
| 5 | 176 | 0.76 | 0.92 | 36 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2899 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2880 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1630 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1575 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 745 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 P48775
- Elsewhere: RCSB PDB 6A4I · PDBe 6A4I · UniProt P48775
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