Research workbench
Crystal structure of human P450 3A4 in complex with ketoconazole
Analyse Crystal structure of human P450 3A4 in complex with ketoconazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V0M
- Type
- protein
- Length
- 1,824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.14.1, 1.14.13.67
- UniProt
- P08684
- Ligands
- KLN, HEM
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A4 (EC 1.14.14.1, 1.14.13.67) | protein | 455 | 52% helix, 9% strand | P08684 |
| B | Cytochrome P450 3A4 (EC 1.14.14.1, 1.14.13.67) | protein | 451 | 52% helix, 9% strand | P08684 |
| C | Cytochrome P450 3A4 (EC 1.14.14.1, 1.14.13.67) | protein | 465 | 52% helix, 9% strand | P08684 |
| D | Cytochrome P450 3A4 (EC 1.14.14.1, 1.14.13.67) | protein | 453 | 51% helix, 9% strand | P08684 |
Ligands and binding sites
- KLN · 1-acetyl-4-(4-{[(2S,4R)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine · ligand · 8 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.86 | 0.87 | 74 | HEM, KLN |
| 2 | 1133 | 0.85 | 0.86 | 74 | HEM, KLN |
| 3 | 1134 | 0.85 | 0.86 | 80 | HEM, KLN |
| 4 | 1156 | 0.85 | 0.86 | 79 | HEM, KLN |
| 5 | 621 | 0.70 | 0.78 | 45 | empty |
Interfaces
5 interfaces between chains.
- B–C · 573 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 552 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 478 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 451 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 277 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 2V0M · PDBe 2V0M · UniProt P08684
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