MolNFT v1 · #94699 · protein
Crystal structure of CYP3A4 ligated to pyridine-substituted desoxyritonavir
4I4H · Cytochrome P450 3A4: “Crystal structure of CYP3A4 ligated to pyridine-substituted desoxyritonavir”. X-ray diffraction, 2 ligands (HEM, Z9Z), 5 pockets (best druggability 0.85). MolNFT v1 #94699 on GenesisL1: 3D structure, binding…
- PDB
- 4I4H
- Type
- protein
- Length
- 457 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.13.-, 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97
- UniProt
- P08684
- Ligands
- HEM, Z9Z
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A4 (EC 1.14.13.-, 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97) | protein | 457 | 54% helix, 10% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- Z9Z · pyridin-3-ylmethyl [(2R,5S)-5-{[N-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-D-valyl]amino}-1,6-diphenylhexan-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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.85 | 0.86 | 75 | HEM, Z9Z |
| 2 | 232 | 0.54 | 0.77 | 33 | empty |
| 3 | 224 | 0.50 | 0.75 | 29 | empty |
| 4 | 165 | 0.50 | 0.77 | 29 | empty |
| 5 | 58 | 0.34 | 0.78 | 15 | empty |
Compared structures
- 4I4H · Crystal structure of CYP3A4 ligated to pyridine-substituted desoxyritonavir · the same entry in another collection · chain A against A, TM-score 1.00
- P08684 · AlphaFold monomer V2.0 prediction for cytochrome P450 3A4 (P08684) · a predicted model of the same protein · chain A 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 P08684
- Elsewhere: RCSB PDB 4I4H · PDBe 4I4H · UniProt P08684
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