Research workbench
Crystal structure of AKR1C1 complexed with glibenclamide
Analyse Crystal structure of AKR1C1 complexed with glibenclamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YVP
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldo-keto reductase family 1 member C1
- EC
- 1.1.1.-, 1.1.1.149, 1.1.1.112, 1.3.1.20
- UniProt
- Q04828
- Ligands
- NAP, GBM
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aldo-keto reductase family 1 member C1 (EC 1.1.1.-, 1.1.1.149, 1.1.1.112, 1.3.1.20) | protein | 318 | 39% helix, 17% strand | Q04828 |
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
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.76 | 0.85 | 45 | NAP, GBM |
| 2 | 375 | 0.76 | 0.86 | 42 | NAP, GBM |
| 3 | 175 | 0.46 | 0.75 | 23 | empty |
| 4 | 134 | 0.46 | 0.77 | 20 | empty |
| 5 | 60 | 0.44 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 294 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4YVP · Crystal Structure of AKR1C1 complexed with glibenclamide · the same entry in another collection · chain A against A, TM-score 1.00
- Q04828 · AlphaFold monomer V2.0 prediction for aldo-keto reductase family 1 member C1 (Q04828) · 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 Q04828
- Elsewhere: RCSB PDB 4YVP · PDBe 4YVP · UniProt Q04828
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