3IBD

Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 3IBD

Classification: Oxidoreductase / Oxidoreductase Inhibitor

Total Structure Weight: 56662.58

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome P450 2B6 A 476 Homo sapiens EC#: 1.14.13 IUBMB
Mutation: Y226H, K262R
Gene Name(s): CYP2B6 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CM5
Query on CM5

A 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL- BETA-D-GLUCOPYRANOSIDE; CYMAL-5 (Synonym)
C23 H42 O11
RVTGFZGNOSKUDA-ZNGNCRBCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CPZ
Query on CPZ

A 4-(4-CHLOROPHENYL)IMIDAZOLE
C9 H7 Cl N2
DVKIFCXVRCGAEE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SCN
Query on SCN

A THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.178
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 89.57 α = 90.00
b = 55.74 β = 96.51
c = 99.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-07-15
  • Released Date: 2010-01-19
  • Deposition author(s): Gay, S.C., Sun, L., Talakad, J.C., Shah, M.B., Stout, D.C., Halpert, J.R.

Revision History

  • 2011-07-13
    Type: Version format compliance
  • 2011-10-26
    Type: Non-polymer description