Research workbench
Crystal structure of trypanosoma cruzi CYP51 bound to the inhibitor (R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4- YLAMINO)PROPAN-2-yl)- 2',3,5'-trifluoro-(1,1'-biphenyl)-4-carboxamide
Analyse Crystal structure of trypanosoma cruzi CYP51 bound to the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BMM
- Type
- protein
- Length
- 1,765 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sterol 14-alpha demethylase
- EC
- 1.14.13.70
- UniProt
- Q7Z1V1
- Ligands
- HEM, TU1
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sterol 14-alpha demethylase (EC 1.14.13.70) | protein | 441 | 54% helix, 11% strand | Q7Z1V1 |
| B | Sterol 14-alpha demethylase (EC 1.14.13.70) | protein | 442 | 53% helix, 12% strand | Q7Z1V1 |
| C | Sterol 14-alpha demethylase (EC 1.14.13.70) | protein | 440 | 54% helix, 12% strand | Q7Z1V1 |
| D | Sterol 14-alpha demethylase (EC 1.14.13.70) | protein | 442 | 52% helix, 12% strand | Q7Z1V1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- TU1 · 4-[2,5-bis(fluoranyl)phenyl]-2-fluoranyl-N-[(2R)-3-(1H-indol-3-yl)-1-oxidanylidene-1-(pyridin-4-ylamino)propan-2-yl]benzamide · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.87 | 0.88 | 86 | HEM, TU1 |
| 2 | 943 | 0.87 | 0.88 | 81 | HEM, TU1 |
| 3 | 908 | 0.86 | 0.88 | 79 | HEM, TU1 |
| 4 | 1148 | 0.86 | 0.86 | 99 | HEM, TU1 |
| 5 | 649 | 0.79 | 0.84 | 75 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1115 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 959 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 447 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4BMM · Crystal structure of Trypanosoma cruzi CYP51 bound to the inhibitor… · the same entry in another collection · chain D against D, TM-score 1.00
- Q7Z1V1 · AlphaFold monomer V2.0 prediction for sterol 14-alpha demethylase (Q7Z1V1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q7Z1V1
- Elsewhere: RCSB PDB 4BMM · PDBe 4BMM · UniProt Q7Z1V1
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