3QU8

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Structures of Cytochrome P450 2B6 Bound to 4-Benzylpyridine and 4-(4-Nitrobenzyl)pyridine: Insight into Inhibitor Binding and Rearrangement of Active Site Side Chains.

Shah, M.B., Pascual, J., Zhang, Q., Stout, C.D., Halpert, J.R.

(2011) Mol Pharmacol 80: 1047-1055

  • DOI: 10.1124/mol.111.074427
  • Primary Citation of Related Structures:  
    3QOA, 3QU8

  • PubMed Abstract: 

    • The biochemical, biophysical, and structural analysis of the cytochrome P450 2B subfamily of enzymes has provided a wealth of information regarding conformational plasticity and substrate recognition. The recent X-ray crystal structure of the drug-metabolizing P450 2B6 in complex with 4-(4-chlorophenyl)imidazole (4-CPI) yielded the first atomic view of this human enzyme ...

    The biochemical, biophysical, and structural analysis of the cytochrome P450 2B subfamily of enzymes has provided a wealth of information regarding conformational plasticity and substrate recognition. The recent X-ray crystal structure of the drug-metabolizing P450 2B6 in complex with 4-(4-chlorophenyl)imidazole (4-CPI) yielded the first atomic view of this human enzyme. However, knowledge of the structural basis of P450 2B6 specificity and inhibition has remained limited. In this study, structures of P450 2B6 were determined in complex with the potent inhibitors 4-benzylpyridine (4-BP) and 4-(4-nitrobenzyl)pyridine (4-NBP). Comparison of the present structures with the previous P450 2B6-4-CPI complex showed that reorientation of side chains of the active site residue Phe206 on the F-helix and Phe297 on the I-helix was necessary to accommodate the inhibitors. However, P450 2B6 does not require any major side chain rearrangement to bind 4-NBP compared with 4-BP, and the enzyme provides no hydrogen-bonding partners for the polar nitro group of 4-NBP within the hydrophobic active site. In addition, on the basis of these new structures, substitution of residue 172 with histidine as observed in the single nucleotide polymorphism Q172H and in P450 2B4 may contribute to a hydrogen bonding network connecting the E- and I-helices, thereby stabilizing active site residues on the I-helix. These results provide insight into the role of active site side chains upon inhibitor binding and indicate that the recognition of the benzylpyridines in the closed conformation structure of P450 2B6 is based solely on hydrophobicity, size, and shape.

    Organizational Affiliation: 

    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093-0703, USA. m7shah@ucsd.edu



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 2B6
A, B, C, D, E, F
A, B, C, D, E, F
476Homo sapiensMutation(s): 11 
Gene Names: CYP2B6
EC: 1.14.14.1 (PDB Primary Data), 1.14.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P20813 (Homo sapiens)
Explore P20813 
Go to UniProtKB:  P20813
PHAROS:  P20813
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20813
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth C],
Q [auth D],
U [auth E],
G [auth A],
J [auth B],
N [auth C],
Q [auth D],
U [auth E],
X [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
CM5
Query on CM5
Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
M [auth B],
P [auth C],
S [auth D],
I [auth A],
L [auth B],
M [auth B],
P [auth C],
S [auth D],
T [auth D],
W [auth E],
Y [auth F]
5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
C23 H42 O11
RVTGFZGNOSKUDA-ZNGNCRBCSA-N		 Ligand Interaction
3QU
Query on 3QU
Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
O [auth C],
R [auth D],
V [auth E]		4-(4-nitrobenzyl)pyridine
C12 H10 N2 O2
MNHKUCBXXMFQDM-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.88α = 90
b = 101.88β = 90
c = 299.509γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
BALBESphasing
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Database references