Research workbench
Crystal structure of the human MGC45594 gene product in complex with diclofenac
Analyse Crystal structure of the human MGC45594 gene product in complex with diclofenac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WEK
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc-binding alcohol dehydrogenase domain-containing protein 2
- EC
- 1.-.-.-
- UniProt
- Q8N4Q0
- Ligands
- DIF, NAP, CL, PO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc-binding alcohol dehydrogenase domain-containing protein 2 (EC 1.-.-.-) | protein | 341 | 34% helix, 27% strand | Q8N4Q0 |
| B | Zinc-binding alcohol dehydrogenase domain-containing protein 2 (EC 1.-.-.-) | protein | 340 | 33% helix, 26% strand | Q8N4Q0 |
Ligands and binding sites
- DIF · 2-[2,6-dichlorophenyl)amino]benzeneacetic acid · ligand · 8 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.79 | 0.84 | 56 | NAP, DIF, GOL, CL |
| 2 | 702 | 0.78 | 0.83 | 58 | NAP, DIF, GOL |
| 3 | 664 | 0.72 | 0.79 | 48 | PO4 |
| 4 | 56 | 0.32 | 0.76 | 11 | DIF |
Interfaces
1 interface between chains.
- A–B · 389 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2WEK · Crystal structure of the human MGC45594 gene product in complex with diclofenac · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N4Q0 · AlphaFold monomer V2.0 prediction for prostaglandin reductase 3 (Q8N4Q0) · a predicted model of the same protein · chain B 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 Q8N4Q0
- Elsewhere: RCSB PDB 2WEK · PDBe 2WEK · UniProt Q8N4Q0
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