MolNFT v1 · #188740 · protein
Crystal structure of human D-amino acid oxidase in complex with inhibitor
7U9S · D-amino-acid oxidase: “Crystal structure of human D-amino acid oxidase in complex with inhibitor”. X-ray diffraction, 2 ligands (FAD, M7I), 6 pockets (best druggability 0.90). MolNFT v1 #188740 on GenesisL1: 3D structure, binding…
- PDB
- 7U9S
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-amino-acid oxidase
- EC
- 1.4.3.3
- UniProt
- P14920
- Ligands
- FAD, M7I
- Pockets
- 6 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-amino-acid oxidase (EC 1.4.3.3) | protein | 338 | 32% helix, 30% strand | P14920 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- M7I · 5-{2-[4-(trifluoromethyl)phenyl]ethyl}-1,4-dihydropyrazine-2,3-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.90 | 0.91 | 135 | FAD, M7I |
| 2 | 814 | 0.80 | 0.83 | 81 | empty |
| 3 | 188 | 0.60 | 0.82 | 24 | empty |
| 4 | 66 | 0.46 | 0.83 | 22 | empty |
| 5 | 55 | 0.42 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 792 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7U9S · Crystal structure of human D-amino acid oxidase in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P14920 · AlphaFold monomer V2.0 prediction for D-amino-acid oxidase (P14920) · a predicted model of the same protein · chain A 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 P14920
- Elsewhere: RCSB PDB 7U9S · PDBe 7U9S · UniProt P14920
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