MolNFT v2 · #185013 · protein
Human CYP3A4 bound to an inhibitor
7KVN · Cytochrome P450 3A4: “Human CYP3A4 bound to an inhibitor”. X-ray diffraction at 2.7, 2 ligands (HEM, X6V), 9 pockets (best druggability 0.86). MolNFT v2 #185013 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KVN
- Type
- protein
- Length
- 900 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.14.1, 1.14.14.56, 1.14.14.73, 1.14.14.55
- UniProt
- P08684
- Ligands
- HEM, X6V
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A4 (EC 1.14.14.1, 1.14.14.56, 1.14.14.73, 1.14.14.55) | protein | 452 | 52% helix, 10% strand | P08684 |
| B | Cytochrome P450 3A4 (EC 1.14.14.1, 1.14.14.56, 1.14.14.73, 1.14.14.55) | protein | 448 | 50% helix, 9% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- X6V · tert-butyl [(2S)-1-(1H-indol-3-yl)-3-{[(2R)-1-oxo-3-phenyl-1-{[3-(pyridin-3-yl)propyl]amino}propan-2-yl]sulfanyl}propan-2-yl]carbamate · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.86 | 0.86 | 74 | HEM, X6V |
| 2 | 1105 | 0.85 | 0.86 | 70 | HEM, X6V |
| 3 | 693 | 0.79 | 0.83 | 62 | empty |
| 4 | 312 | 0.58 | 0.77 | 47 | empty |
| 5 | 108 | 0.55 | 0.83 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 417 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 P08684
- Elsewhere: RCSB PDB 7KVN · PDBe 7KVN · UniProt P08684
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