MolNFT v1 · #134748 · protein
Crystal structure of the midazolam-bound human CYP3A4
5TE8 · Cytochrome P450 3A4: “Crystal structure of the midazolam-bound human CYP3A4”. X-ray diffraction, 2 ligands (HEM, 08J), 15 pockets (best druggability 0.86). MolNFT v1 #134748 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5TE8
- Type
- protein
- Length
- 1,410 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.13.-
- UniProt
- P08684
- Ligands
- HEM, 08J
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A4 (EC 1.14.13.-) | protein | 470 | 49% helix, 9% strand | P08684 |
| B | Cytochrome P450 3A4 (EC 1.14.13.-) | protein | 471 | 48% helix, 9% strand | P08684 |
| C | Cytochrome P450 3A4 (EC 1.14.13.-) | protein | 469 | 46% helix, 9% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- 08J · 8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.86 | 0.89 | 73 | HEM, 08J |
| 2 | 839 | 0.86 | 0.88 | 83 | HEM, 08J |
| 3 | 925 | 0.85 | 0.87 | 95 | HEM, 08J |
| 4 | 779 | 0.84 | 0.87 | 77 | empty |
| 5 | 1072 | 0.79 | 0.81 | 65 | empty |
Interfaces
2 interfaces between chains.
- A–C · 677 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 560 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 5TE8 · PDBe 5TE8 · UniProt P08684
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