Research workbench
Crystal structure of human P450 2C9*2 genetic variant in complex with losartan
Analyse Crystal structure of human P450 2C9*2 genetic variant in complex with losartan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VLT
- Type
- protein
- Length
- 3,684 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2C9
- EC
- 1.14.14.1, 1.14.14.53, 1.14.14.51, 1.14.14.52
- UniProt
- P11712
- Ligands
- HEM, LSN, CM5, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2C9 (EC 1.14.14.1, 1.14.14.53, 1.14.14.51, 1.14.14.52) | protein | 461 | 52% helix, 8% strand | P11712 |
| B | Cytochrome P450 2C9 (EC 1.14.14.1, 1.14.14.53, 1.14.14.51, 1.14.14.52) | protein | 461 | 52% helix, 9% strand | P11712 |
| C, E, F | Cytochrome P450 2C9 (EC 1.14.14.1, 1.14.14.53, 1.14.14.51, 1.14.14.52) | protein | 460 | 53% helix, 8% strand | P11712 |
| D | Cytochrome P450 2C9 (EC 1.14.14.1, 1.14.14.53, 1.14.14.51, 1.14.14.52) | protein | 461 | 52% helix, 9% strand | P11712 |
| G | Cytochrome P450 2C9 (EC 1.14.14.1, 1.14.14.53, 1.14.14.51, 1.14.14.52) | protein | 462 | 52% helix, 9% strand | P11712 |
| H | Cytochrome P450 2C9 (EC 1.14.14.1, 1.14.14.53, 1.14.14.51, 1.14.14.52) | protein | 459 | 52% helix, 9% strand | P11712 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- LSN · [2-butyl-5-chloranyl-3-[[4-[2-(2H-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]imidazol-4-yl]methanol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CM5 · 5-cyclohexyl-1-pentyl-beta-D-maltoside · ligand · 8 copies · chains A, E, F, B, C, G, D, H
- SO4 · Sulfate ion · ion · 3 copies · chains E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.89 | 0.92 | 80 | HEM, LSN |
| 2 | 752 | 0.89 | 0.92 | 73 | HEM, LSN |
| 3 | 745 | 0.89 | 0.92 | 71 | HEM, LSN |
| 4 | 818 | 0.88 | 0.91 | 80 | HEM, LSN |
| 5 | 815 | 0.88 | 0.91 | 86 | HEM, LSN |
Interfaces
11 interfaces between chains.
- C–F · 426 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 421 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 372 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 359 Ų buried · 0 hydrogen bonds · protein-protein
- D–H · 358 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6VLT · Crystal Structure of Human P450 2C9*2 Genetic Variant in Complex with Losartan · the same entry in another collection · chain H against H, TM-score 1.00
- P11712 · AlphaFold monomer V2.0 prediction for cytochrome P450 2C9 (P11712) · a predicted model of the same protein · chain H 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 P11712
- Elsewhere: RCSB PDB 6VLT · PDBe 6VLT · UniProt P11712
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