Research workbench
Crystal structure of sterol 14-alpha demethylase (CYP51) from trypanosoma brucei bound to an inhibitor N-(1-(2,4-dichlorophenyl)-2- (1H-imidazol-1-YL)ETHYL)-4-(5-phenyl-1,3,4-oxaziazol-2-YL)BENZAMIDE
Analyse Crystal structure of sterol 14-alpha demethylase (CYP51) from trypanosoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GW9
- Type
- protein
- Length
- 1,797 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sterol 14ALPHA-demethylase
- EC
- 1.14.13.70
- UniProt
- Q385E8
- Ligands
- HEM, VNI
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sterol 14ALPHA-demethylase (EC 1.14.13.70) | protein | 450 | 54% helix, 12% strand | Q385E8 |
| B, C, D | Sterol 14ALPHA-demethylase (EC 1.14.13.70) | protein | 449 | 54% helix, 12% strand | Q385E8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- VNI · N-[(1R)-1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl]-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.89 | 0.91 | 81 | HEM, VNI |
| 2 | 1152 | 0.87 | 0.88 | 91 | HEM, VNI |
| 3 | 928 | 0.85 | 0.86 | 75 | HEM, VNI |
| 4 | 1022 | 0.85 | 0.85 | 86 | HEM, VNI |
| 5 | 1001 | 0.81 | 0.83 | 75 | empty |
Interfaces
5 interfaces between chains.
- C–D · 995 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 805 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 687 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 407 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 312 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3GW9 · Crystal structure of sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei bound to… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q385E8
- Elsewhere: RCSB PDB 3GW9 · PDBe 3GW9 · UniProt Q385E8
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