Research workbench

Naegleria fowleri CYP51-ketoconazole complex

Analyse Naegleria fowleri CYP51-ketoconazole complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AYB
Type: protein
Length: 449 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CYP51, sterol 14ALPHA-demethylase
Ligands: HEM, KKK, CA
Pockets: 4 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CYP51, sterol 14ALPHA-demethylase	protein	449	56% helix, 11% strand	—

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
KKK · 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine · ligand · chains A
CA · Calcium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 5 copies · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	759	0.86	0.89	68	HEM, KKK
2	294	0.60	0.79	32	EDO
3	127	0.47	0.78	27	EDO
4	53	0.26	0.73	13	empty

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

6AYB · Naegleria fowleri CYP51-ketoconazole complex · 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
Elsewhere: RCSB PDB 6AYB · PDBe 6AYB

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