Research workbench
Crystal structure of CYP124 in complex with inhibitor compound 5'
Analyse Crystal structure of CYP124 in complex with inhibitor compound 5' in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T0L
- Type
- protein
- Length
- 422 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CYP124 in complex with inhibitor compound 5'
- UniProt
- P9WPP3
- Ligands
- HEM, M8N, CL
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CYP124 in complex with inhibitor compound 5' | protein | 422 | 51% helix, 12% strand | P9WPP3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- M8N · ~{N}-[[[2-methyl-4-(3-methylbutyl) phenyl]amino]methyl]hydroxylamine · ligand · chains A
- CL · Chloride ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.88 | 0.92 | 71 | HEM, M8N |
| 2 | 168 | 0.72 | 0.90 | 35 | empty |
| 3 | 60 | 0.42 | 0.82 | 17 | empty |
| 4 | 66 | 0.29 | 0.73 | 16 | empty |
Compared structures
- 6T0L · Crystal structure of CYP124 in complex with inhibitor compound 5' · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPP3 · AlphaFold monomer V2.0 prediction for methyl-branched lipid omega- hydroxylase (P9WPP3) · a predicted model of the same protein · chain A 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 P9WPP3
- Elsewhere: RCSB PDB 6T0L · PDBe 6T0L · UniProt P9WPP3
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