Research workbench

Clotrimazole complex of cytochrome P450 46A1

Analyse Clotrimazole complex of cytochrome P450 46A1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MDV
Type: protein
Length: 848 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cholesterol 24-hydroxylase
EC: 1.14.13.98
UniProt: Q9Y6A2
Ligands: HEM, CL6
Pockets: 14 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cholesterol 24-hydroxylase (EC 1.14.13.98)	protein	424	54% helix, 13% strand	Q9Y6A2

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
CL6 · 1-[(2-chlorophenyl)(diphenyl)methyl]-1H-imidazole · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	561	0.87	0.92	53	HEM, CL6
2	760	0.86	0.88	76	HEM, CL6
3	674	0.77	0.82	53	empty
4	152	0.56	0.82	20	empty
5	151	0.56	0.82	18	empty

Interfaces

1 interface between chains.

A–B · 583 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3MDV · Clotrimazole complex of Cytochrome P450 46A1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y6A2 · AlphaFold monomer V2.0 prediction for cholesterol 24-hydroxylase (Q9Y6A2) · 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 Q9Y6A2
Elsewhere: RCSB PDB 3MDV · PDBe 3MDV · UniProt Q9Y6A2

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