Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 54989.01 
• Atom Count: 3769 
• Residue Count: 473 
• Unique protein chains: 1

1NR6

MICROSOMAL CYTOCHROME P450 2C5/3LVDH COMPLEX WITH DICLOFENAC

• DOI: 10.2210/pdb1NR6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli
• Mutation(s): 5 


• Deposited: 2003-01-23 Released: 2003-08-12 
• Deposition Author(s): Wester, M.R., Johnson, E.F., Stout, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.268 
• R-Value Work: 0.231 

Literature

Structure of Mammalian Cytochrome P450 2C5 Complexed with Diclofenac at 2.1 A Resolution: Evidence for an Induced Fit Model of Substrate Binding

WESTER, M.R., JOHNSON, E.F., Marques-Soares, C., Dijols, S., Dansette, P.M., Mansuy, D., STOUT, C.D.

(2003) Biochemistry 42: 9335-9345

• PubMed: 12899620 
• DOI: 10.1021/bi034556l


• PubMed Abstract: 
  

The structure of the anti-inflammatory drug diclofenac bound in the active site of rabbit microsomal cytochrome P450 2C5/3LVdH was determined by X-ray crystallography to 2.1 A resolution. P450 2C5/3LVdH and the related enzyme 2C5dH catalyze the 4'-hydroxylation of diclofenac with apparent K(m) values of 80 and 57 microM and k(cat) values of 13 and 16 min(-1), respectively. Spectrally determined binding constants are similar to the K(m) values. The structure indicates that the pi-electron system of the dichlorophenyl moiety faces the heme Fe with the 3'- and 4'-carbons located 4.4 and 4.7 A, respectively, from the Fe. The carboxyl moiety of the substrate is hydrogen bonded to a cluster of waters that are also hydrogen bonded to the side chains of N204, K241, S289, and D290 as well as the backbone of the protein. The proximity of the diclofenac carboxylate to the side chain of D290 together with an increased binding affinity at lower pH suggests that diclofenac is protonated when bound to the enzyme. The structure exhibits conformational changes indicative of an adaptive fit to the substrate reflecting both the hydration and size of the substrate. These results indicate how structurally diverse substrates are recognized by drug-metabolizing P450 enzymes.

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Organizational Affiliation: 

Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MEM-255, La Jolla, California 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CYTOCHROME P450 2C5	A	473	Oryctolagus cuniculus	Mutation(s): 13  Gene Names: CYP2C5 EC: 1.14.14.1
Find proteins for P00179 (Oryctolagus cuniculus) Go to UniProtKB:  P00179

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DIF	A	2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID DICLOFENAC C14 H11 Cl2 N O2 DCOPUUMXTXDBNB-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DIF	Kd: ~50000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.268 
• R-Value Work: 0.231 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 73.940	α = 90.00
b = 130.020	β = 90.00
c = 172.780	γ = 90.00

Software Package:

Software Name	Purpose
CNS	phasing
CCP4	data scaling
MOSFLM	data reduction
Blu-Ice	data collection
CNS	refinement
SSRL	data collection
CCP4	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-23 
• Released Date: 2003-08-12 
• Deposition Author(s): Wester, M.R., Johnson, E.F., Stout, C.D.

Revision History 

• Version 1.0: 2003-08-12
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance