5A5I | pdb_00005a5i

Cytochrome 2C9 P450 inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb5A5I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-18 Released: 2016-08-24 
• Deposition Author(s): Skerratt, S.E., de Groot, M.J., Phillips, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Discovery of a Novel Binding Pocket for Cyp 2C9 Inhibitors: Crystallography, Pharmacophore Modelling and Inhibitor Sar.

Skerratt, S.E., de Groot, M.J., Phillips, C.

(2016) Medchemcomm 7: 813

• DOI: https://doi.org/10.1039/C6MD00011H

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.32 kDa 
• Atom Count: 3,702 
• Modeled Residue Count: 453 
• Deposited Residue Count: 477 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 2C9	A	477	Homo sapiens	Mutation(s): 0  EC: 1.14.14.1 (UniProt), 1.14.14.53 (UniProt), 1.14.14.52 (UniProt), 1.14.14.51 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11712 (Homo sapiens) Explore P11712  Go to UniProtKB:  P11712
PHAROS:  P11712 GTEx:  ENSG00000138109

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
XI1	B [auth A]	N-[4-(3-chloranyl-4-cyano-phenoxy)cyclohexyl]-1,1,1-tris(fluoranyl)methanesulfonamide C14 H14 Cl F3 N2 O3 S AMFHXCAGSKYZAM-XYPYZODXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.217	α = 90
b = 92.217	β = 90
c = 170.414	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-24 
Deposition Author(s): Skerratt, S.E., de Groot, M.J., Phillips, C.

Revision History  

• Version 1.0: 2016-08-24
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other