MolNFT v1 · #108659 · protein
17BETA-HSD5 in complex with 3,6-dihydropyridin-1(2H)-YL(5-methyl-1H- indol-2-YL)METHANONE
4WDW · Aldo-keto reductase family 1 member C3: “17BETA-HSD5 in complex with 3,6-dihydropyridin-1(2H)-YL(5-methyl-1H- indol-2-YL)METHANONE”. X-ray diffraction, 2 ligands (NAP, WDW), 4 pockets (best druggability 0.77). MolNFT v1 #108659 on…
- PDB
- 4WDW
- Type
- protein
- Length
- 599 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldo-keto reductase family 1 member C3
- EC
- 1.1.1.64
- UniProt
- P42330
- Ligands
- NAP, WDW
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldo-keto reductase family 1 member C3 (EC 1.1.1.64) | protein | 298 | 41% helix, 17% strand | P42330 |
| B | Aldo-keto reductase family 1 member C3 (EC 1.1.1.64) | protein | 301 | 42% helix, 18% strand | P42330 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- WDW · 3,6-dihydropyridin-1(2H)-yl(5-methyl-1H-indol-2-yl)methanone · ligand · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.77 | 0.80 | 80 | NAP, WDW |
| 2 | 484 | 0.72 | 0.81 | 50 | NAP, WDW |
| 3 | 87 | 0.37 | 0.76 | 20 | empty |
| 4 | 78 | 0.32 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 406 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4WDW · 17beta-HSD5 in complex with 3,6-dihydropyridin-1(2H)-yl(5-methyl-1H-indol-2-yl)metha · the same entry in another collection · chain A against A, TM-score 1.00
- P42330 · AlphaFold monomer V2.0 prediction for aldo-keto reductase family 1 member C3 (P42330) · a predicted model of the same protein · chain A 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 P42330
- Elsewhere: RCSB PDB 4WDW · PDBe 4WDW · UniProt P42330
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