4NZ2

Crystal structure of CYP2C9 in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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

  • DOI: 10.1016/j.drudis.2014.03.012
  • Primary Citation of Related Structures:  
    4NY4, 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 ...

    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.


    Organizational Affiliation

    Discovery Sciences, AstraZeneca R&D Mölndal, Mölndal S-431 83, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 2C9A, B475Homo sapiensMutation(s): 7 
Gene Names: CYP2C10CYP2C9CYP2C9 CYP2C10
EC: 1.14.13 (PDB Primary Data), 1.14.13.80 (PDB Primary Data), 1.14.13.48 (PDB Primary Data), 1.14.13.49 (PDB Primary Data), 1.14.14.1 (UniProt), 1.14.14.53 (UniProt), 1.14.14.51 (UniProt), 1.14.14.52 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11712 (Homo sapiens)
Explore P11712 
Go to UniProtKB:  P11712
PHAROS:  P11712
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A], G [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
2QJ
Query on 2QJ

Download Ideal Coordinates CCD File 
F [auth A], J [auth B](2R)-N-{4-[(3-bromophenyl)sulfonyl]-2-chlorophenyl}-3,3,3-trifluoro-2-hydroxy-2-methylpropanamide
C16 H12 Br Cl F3 N O4 S
NPCYFKFOPWAEFV-OAHLLOKOSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], I [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A], H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2QJKd:  2000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.38α = 90
b = 164.38β = 90
c = 111.59γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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