Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56432.25 
• Atom Count: 3777 
• Residue Count: 484 
• Unique protein chains: 1

4NY4

Crystal structure of CYP3A4 in complex with an inhibitor

• DOI: 10.2210/pdb4NY4/pdb

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


• Deposited: 2013-12-10 Released: 2014-08-13 
• Deposition Author(s): Branden, G., Sjogren, T., Xue, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.273 
• R-Value Work: 0.249 

Literature

Structure-based ligand design to overcome CYP inhibition in drug discovery projects.

Branden, G., Sjogren, T., Schnecke, V., Xue, Y.

(2014) Drug Discov Today 19: 905-911

• PubMed: 24642031 
• DOI: 10.1016/j.drudis.2014.03.012
• Primary Citation of Related Structures:  
  4NZ2


• PubMed Abstract: 
  

Cytochrome P450 (CYP) enzymes are key players in xenobiotic metabolism, and inhibition of CYPs can therefore result in unwanted drug-drug interactions. Within drug discovery, CYP inhibition can cause delays in the progression of candidate drugs, or even premature closure of projects. During the past decade, a massive effort in the pharmaceutical industry and academic research has produced a wealth of structural information in the CYP field. In this short review, we will describe how structure-based approaches can be used in the pharmaceutical industry to work away from CYP inhibition, with a focus on the opportunities and challenges. We will show two examples from our own work where structural information on CYP2C9 and CYP3A4 inhibitor complexes have been successfully exploited in ongoing drug discovery projects.

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Organizational Affiliation: 

Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg S-405 30, Sweden. Electronic address: [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome P450 3A4	A	484	Homo sapiens	Mutation(s): 0  Gene Names: CYP3A4 (CYP3A3) EC: 1.14.14.-
Find proteins for P08684 (Homo sapiens) Go to Gene View: CYP3A4 Go to UniProtKB:  P08684

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
2QH	A	(8R)-3,3-difluoro-8-[4-fluoro-3-(pyridin-3-yl)phenyl]-8-(4-methoxy-3-methylphenyl)-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine C25 H22 F3 N5 O YGQLOGGNUHAJMB-RUZDIDTESA-N
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.273 
• R-Value Work: 0.249 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 78.548	α = 90.00
b = 101.692	β = 90.00
c = 132.422	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHASER	phasing
BUSTER-TNT	refinement
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-10 
• Released Date: 2014-08-13 
• Deposition Author(s): Branden, G., Sjogren, T., Xue, Y.

Revision History 

• Version 1.0: 2014-08-13
  Type: Initial release