MolNFT v1 · #111609 · protein
Crystal structure of AKR1C3 complexed with glibenclamide
4YVV · Aldo-keto reductase family 1 member C3: “Crystal structure of AKR1C3 complexed with glibenclamide”. X-ray diffraction, 2 ligands (NAP, GBM), 6 pockets (best druggability 0.79). MolNFT v1 #111609 on GenesisL1: 3D structure, binding…
- PDB
- 4YVV
- Type
- protein
- Length
- 630 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.-.-.-, 1.1.1.357, 1.1.1.112, 1.1.1.188, 1.1.1.239, 1.1.1.64, 1.3.1.20
- UniProt
- P42330
- Ligands
- NAP, GBM
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aldo-keto reductase family 1 member C3 (EC 1.-.-.-, 1.1.1.357, 1.1.1.112, 1.1.1.188, 1.1.1.239, 1.1.1.64, 1.3.1.20) | protein | 315 | 41% helix, 17% strand | P42330 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- GBM · 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl) sulfamoyl]phenyl}ethyl)-2-methoxybenzamide · 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 | 606 | 0.79 | 0.85 | 62 | NAP, GBM |
| 2 | 626 | 0.79 | 0.84 | 56 | NAP, GBM |
| 3 | 240 | 0.54 | 0.77 | 34 | empty |
| 4 | 230 | 0.50 | 0.75 | 29 | empty |
| 5 | 74 | 0.32 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 380 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4YVV · Crystal structure of AKR1C3 complexed with glibenclamide · 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 4YVV · PDBe 4YVV · UniProt P42330
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