MolNFT v1 · #108660 · protein
17BETA-HSD5 in complex with [4-(2-HYDROXYETHYL)PIPERIDIN-1-YL](5- methyl-1H-indol-2-YL)METHANONE
4WDX · Aldo-keto reductase family 1 member C3: “17BETA-HSD5 in complex with [4-(2-HYDROXYETHYL)PIPERIDIN-1-YL](5- methyl-1H-indol-2-YL)METHANONE”. X-ray diffraction, 2 ligands (NAP, WDX), 4 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 4WDX
- Type
- protein
- Length
- 600 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, WDX
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% 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 | 43% helix, 17% strand | P42330 |
| B | Aldo-keto reductase family 1 member C3 (EC 1.1.1.64) | protein | 302 | 41% helix, 18% strand | P42330 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- WDX · [4-(2-hydroxyethyl)piperidin-1-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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.78 | 0.87 | 50 | NAP, WDX |
| 2 | 441 | 0.78 | 0.86 | 55 | NAP, WDX |
| 3 | 615 | 0.69 | 0.78 | 55 | empty |
| 4 | 60 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 445 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4WDX · 17beta-HSD5 in complex with [4-(2-hydroxyethyl)piperidin-1-yl](5-methyl-1H-indol-2-yl)meth… · 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 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 P42330
- Elsewhere: RCSB PDB 4WDX · PDBe 4WDX · UniProt P42330
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