MolNFT v1 · #88843 · protein
Cytochrome P450 3A4 bound to an inhibitor
4D7D: “Cytochrome P450 3A4 bound to an inhibitor”. X-ray diffraction, 2 ligands (HEM, PKT), 5 pockets (best druggability 0.85). MolNFT v1 #88843 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4D7D
- Type
- protein
- Length
- 458 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97
- UniProt
- P08684
- Ligands
- HEM, PKT
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A4 (EC 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97) | protein | 458 | 51% helix, 9% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- PKT · tert-butyl [(2S)-1-(1H-indol-3-yl)-3-({3-oxo-3-[(pyridin-3-ylmethyl)amino]propyl}sulfanyl)propan-2-yl]carbamate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.85 | 0.85 | 83 | HEM, PKT |
| 2 | 246 | 0.53 | 0.76 | 40 | empty |
| 3 | 208 | 0.49 | 0.75 | 28 | empty |
| 4 | 98 | 0.40 | 0.76 | 16 | empty |
| 5 | 54 | 0.29 | 0.75 | 14 | empty |
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 4D7D · PDBe 4D7D · UniProt P08684
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