MolNFT v1 · #94846 · protein
Human cytochrome P450 1A1 in complex with alpha-naphthoflavone
4I8V: “Human cytochrome P450 1A1 in complex with alpha-naphthoflavone”. X-ray diffraction, 3 ligands (HEM, BHF, NO3), 20 pockets (best druggability 0.87). MolNFT v1 #94846 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4I8V
- Type
- protein
- Length
- 1,884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 1A1
- EC
- 1.14.14.1
- UniProt
- P04798
- Ligands
- HEM, BHF, NO3
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 1A1 (EC 1.14.14.1) | protein | 477 | 53% helix, 10% strand | P04798 |
| B | Cytochrome P450 1A1 (EC 1.14.14.1) | protein | 472 | 52% helix, 10% strand | P04798 |
| C | Cytochrome P450 1A1 (EC 1.14.14.1) | protein | 468 | 53% helix, 7% strand | P04798 |
| D | Cytochrome P450 1A1 (EC 1.14.14.1) | protein | 467 | 53% helix, 10% strand | P04798 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- BHF · 2-phenyl-4H-benzo[h]chromen-4-one · ligand · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.87 | 0.93 | 57 | HEM, BHF |
| 2 | 469 | 0.86 | 0.93 | 54 | HEM, BHF |
| 3 | 484 | 0.86 | 0.93 | 61 | HEM, BHF |
| 4 | 483 | 0.86 | 0.93 | 55 | HEM, BHF |
| 5 | 697 | 0.68 | 0.76 | 69 | empty |
Interfaces
3 interfaces between chains.
- A–B · 674 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 510 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 234 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 P04798
- Elsewhere: RCSB PDB 4I8V · PDBe 4I8V · UniProt P04798
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