MolNFT v1 · #71420 · protein

Voriconazole complex of cytochrome P450 46A1

3MDT · Cholesterol 24-hydroxylase: “Voriconazole complex of cytochrome P450 46A1”. X-ray diffraction, 2 ligands (HEM, VOR), 13 pockets (best druggability 0.88). MolNFT v1 #71420 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3MDT
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, VOR
Pockets: 13 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cholesterol 24-hydroxylase (EC 1.14.13.98)	protein	424	53% helix, 13% strand	Q9Y6A2

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
VOR · Voriconazole · ligand · 2 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	612	0.88	0.93	57	HEM, VOR
2	632	0.88	0.92	55	HEM, VOR
3	720	0.76	0.81	61	empty
4	80	0.58	0.87	15	empty
5	173	0.56	0.81	25	empty

Interfaces

1 interface between chains.

A–B · 603 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3MDT · Voriconazole 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 B 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 3MDT · PDBe 3MDT · UniProt Q9Y6A2

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