MolNFT v1 · #109018 · protein
X-ray crystal structure of CYP119 complexed with 4-(4-flourophenyl)- 1H-imidazole
4WPD · Cytochrome P450 119: “X-ray crystal structure of CYP119 complexed with 4-(4-flourophenyl)- 1H-imidazole”. X-ray diffraction, 2 ligands (3SQ, HEM), 10 pockets (best druggability 0.86). MolNFT v1 #109018 on GenesisL1: 3D structure…
- PDB
- 4WPD
- Type
- protein
- Length
- 734 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 119
- EC
- 1.14.-.-, 1.11.1.7
- UniProt
- Q55080
- Ligands
- 3SQ, HEM
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome P450 119 (EC 1.14.-.-, 1.11.1.7) | protein | 367 | 49% helix, 13% strand | Q55080 |
Ligands and binding sites
- 3SQ · 4-(4-fluorophenyl)-1H-imidazole · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.86 | 0.92 | 47 | HEM, 3SQ |
| 2 | 774 | 0.85 | 0.88 | 80 | 3SQ, HEM |
| 3 | 501 | 0.83 | 0.89 | 52 | empty |
| 4 | 120 | 0.51 | 0.81 | 20 | empty |
| 5 | 155 | 0.50 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1628 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4WPD · X-ray Crystal Structure of CYP119 complexed with 4-(4-flourophenyl)-1H-imidazole · the same entry in another collection · chain A against A, TM-score 1.00
- Q55080 · AlphaFold monomer V2.0 prediction for cytochrome P450 119 (Q55080) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q55080
- Elsewhere: RCSB PDB 4WPD · PDBe 4WPD · UniProt Q55080
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