Research workbench
Co-crystal structure of compound 3 (4-hydroxy-6-[2-(7-hydroxy-2-oxo-4- phenyl-2H-chromen-6-YL)ETHYL]PYRIDAZIN-3(2H)-one) and FAD bound to human daao at 2.4A
Analyse Co-crystal structure of compound 3 (4-hydroxy-6-[2-(7-hydroxy-2-oxo-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QFC
- Type
- protein
- Length
- 653 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, 31T, K
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-amino-acid oxidase (EC 1.4.3.3) | protein | 330 | 34% helix, 29% strand | P14920 |
| B | D-amino-acid oxidase (EC 1.4.3.3) | protein | 323 | 33% helix, 29% strand | P14920 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 31T · 4-hydroxy-6-[2-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)ethyl]pyridazin-3(2H)-one · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.86 | 0.91 | 71 | FAD, 31T |
| 2 | 599 | 0.85 | 0.90 | 80 | FAD, 31T |
| 3 | 61 | 0.71 | 0.97 | 20 | empty |
| 4 | 204 | 0.59 | 0.80 | 34 | empty |
| 5 | 133 | 0.50 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1573 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4QFC · Co-crystal structure of compound 3 (4-hydroxy-6-[2-(7-hydroxy-2-oxo-4-phenyl-2h-chromen-6… · 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 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 P14920
- Elsewhere: RCSB PDB 4QFC · PDBe 4QFC · UniProt P14920
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