MolNFT v1 · #73297 · protein
Crystal structure of human cytochrome P4503A4 bound to an inhibitor ritonavir
3NXU · Cytochrome P450 3A4: “Crystal structure of human cytochrome P4503A4 bound to an inhibitor ritonavir”. X-ray diffraction, 2 ligands (HEM, RIT), 12 pockets (best druggability 0.86). MolNFT v1 #73297 on GenesisL1: 3D structure, binding…
- PDB
- 3NXU
- Type
- protein
- Length
- 914 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.13.67, 1.14.13.97, 1.14.13.32
- UniProt
- P08684
- Ligands
- HEM, RIT
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome P450 3A4 (EC 1.14.13.67, 1.14.13.97, 1.14.13.32) | protein | 457 | 54% helix, 9% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- RIT · Ritonavir · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.86 | 0.86 | 74 | HEM, RIT |
| 2 | 1156 | 0.85 | 0.85 | 73 | HEM, RIT |
| 3 | 964 | 0.74 | 0.77 | 68 | empty |
| 4 | 619 | 0.73 | 0.80 | 34 | empty |
| 5 | 132 | 0.55 | 0.82 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 371 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3NXU · Crystal structure of human cytochrome P4503A4 bound to an inhibitor ritonavir · 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 3NXU · PDBe 3NXU · UniProt P08684
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