MolNFT v1 · #180316 · protein
Human CYP3A4 bound to an inhibitor
7KVS · Cytochrome P450 3A4: “Human CYP3A4 bound to an inhibitor”. X-ray diffraction, 3 ligands (HEM, X74, SO4), 10 pockets (best druggability 0.85). MolNFT v1 #180316 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KVS
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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, X74, SO4
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 9% 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 | 457 | 51% helix, 9% strand | P08684 |
| B | Cytochrome P450 3A4 (EC 1.14.14.1, 1.14.14.56, 1.14.14.73, 1.14.14.55) | protein | 441 | 52% helix, 10% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- X74 · tert-butyl [(2R)-1-(naphthalen-1-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
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.85 | 0.86 | 71 | HEM, X74 |
| 2 | 1181 | 0.85 | 0.85 | 72 | HEM, X74 |
| 3 | 479 | 0.70 | 0.80 | 54 | empty |
| 4 | 364 | 0.65 | 0.79 | 39 | EDO |
| 5 | 294 | 0.58 | 0.77 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 331 Ų buried · 0 hydrogen bonds · 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 7KVS · PDBe 7KVS · UniProt P08684
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