Research workbench
Complex of human CYP3A4 with a desoxyritonavir analog
Analyse Complex of human CYP3A4 with a desoxyritonavir analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K9W
- Type
- protein
- Length
- 1,831 residues
- Chains
- 4
- 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, 7AW
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 9% 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 | 458 | 54% helix, 9% strand | P08684 |
| B | 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 | 53% helix, 9% strand | P08684 |
| C, D | Cytochrome P450 3A4 (EC 1.14.13.-, 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97) | protein | 458 | 53% helix, 10% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- 7AW · N~2~-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-N-[(2R,5S)-1-phenyl-5-{[(1,3-thiazol-5-ylmethoxy)carbonyl]amino}octan-2-yl]-L-valinamide · 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 | 1184 | 0.86 | 0.87 | 88 | HEM, 7AW |
| 2 | 1162 | 0.86 | 0.87 | 95 | HEM, 7AW |
| 3 | 1190 | 0.86 | 0.86 | 82 | HEM, 7AW |
| 4 | 1132 | 0.86 | 0.86 | 78 | HEM, 7AW |
| 5 | 1114 | 0.80 | 0.81 | 86 | empty |
Interfaces
5 interfaces between chains.
- C–D · 404 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 352 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 218 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 151 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 102 Ų buried · 2 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 4K9W · PDBe 4K9W · UniProt P08684
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