3QOA

Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with the inhibitor 4-Benzylpyridine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 3QOA

Classification: OXIDOREDUCTASE / OXIDOREDUCTASE INHIBITOR

Total Structure Weight: 56420.86

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome P450 2B6 A 476 Homo sapiens EC#: 1.14.13 IUBMB
Fragment: Cytochrome P450 2B6, residues 3-21 deleted
Mutation: E2A, R22K, H23K, P24T, N25S, T26S, H27K, D28G, R29K, Y226H, K262R
Gene Name(s): CYP2B6 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 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)
3QO
Query on 3QO

A 4-benzylpyridine
C12 H11 N
DBOLXXRVIFGDTI-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3QO N/A in BindingDB
Kd: 210 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.197
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 76.76 α = 90.00
b = 76.76 β = 90.00
c = 201.34 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-02-09
  • Released Date: 2011-09-14
  • Deposition author(s): Shah, M.B., Pascual, J., Stout, C.D., Halpert, J.R.

Revision History

  • 2011-12-07
    Type: Database references