Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110104.73 
• Atom Count: 7484 
• Residue Count: 922 
• Unique protein chains: 1

3LD6

Crystal structure of human lanosterol 14alpha-demethylase (CYP51) in complex with ketoconazole

• DOI: 10.2210/pdb3LD6/pdb
• Entry 3LD6 supersedes 3I3K

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2010-01-12 Released: 2010-02-02 
• Deposition Author(s): Strushkevich, N., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.275 
• R-Value Work: 0.212 

Literature

Structural basis of human CYP51 inhibition by antifungal azoles.

Strushkevich, N., Usanov, S.A., Park, H.W.

(2010) J.Mol.Biol. 397: 1067-1078

• PubMed: 20149798 
• DOI: 10.1016/j.jmb.2010.01.075
• Primary Citation of Related Structures:  
  3JUV, 3JUS


• PubMed Abstract: 
  

The obligatory step in sterol biosynthesis in eukaryotes is demethylation of sterol precursors at the C14-position, which is catalyzed by CYP51 (sterol 14-alpha demethylase) in three sequential reactions. In mammals, the final product of the pathway is cholesterol, while important intermediates, meiosis-activating sterols, are produced by CYP51. Three crystal structures of human CYP51, ligand-free and complexed with antifungal drugs ketoconazole and econazole, were determined, allowing analysis of the molecular basis for functional conservation within the CYP51 family. Azole binding occurs mostly through hydrophobic interactions with conservative residues of the active site. The substantial conformational changes in the B' helix and F-G loop regions are induced upon ligand binding, consistent with the membrane nature of the protein and its substrate. The access channel is typical for mammalian sterol-metabolizing P450 enzymes, but is different from that observed in Mycobacterium tuberculosis CYP51. Comparison of the azole-bound structures provides insight into the relative binding affinities of human and bacterial P450 enzymes to ketoconazole and fluconazole, which can be useful for the rational design of antifungal compounds and specific modulators of human CYP51.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, Canada. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lanosterol 14-alpha demethylase	A, B	461	Homo sapiens	Mutation(s): 0  Gene Names: CYP51A1 (CYP51) EC: 1.14.14.154
Find proteins for Q16850 (Homo sapiens) Go to Gene View: CYP51A1 Go to UniProtKB:  Q16850

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
KKK	A, B	1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine C26 H28 Cl2 N4 O4 XMAYWYJOQHXEEK-OZXSUGGESA-N
BCD	A, B	BETA-CYCLODEXTRIN CYCLO-HEPTA-AMYLOSE C42 H70 O35 WHGYBXFWUBPSRW-FOUAGVGXSA-N
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.275 
• R-Value Work: 0.212 
• Space Group: P 4 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 145.726	α = 90.00
b = 145.726	β = 90.00
c = 110.341	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data collection
CCP4	phasing
REFMAC	refinement
CCP4	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-12 
• Released Date: 2010-02-02 
• Deposition Author(s): Strushkevich, N., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H., Structural Genomics Consortium (SGC)
• This entry supersedes: 3I3K

Revision History 

• Version 1.0: 2010-02-02
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2018-01-24
  Type: Structure summary
• Version 1.3: 2018-04-18
  Type: Data collection