4JLT

Crystal structure of P450 2B4(H226Y) in complex with paroxetine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Structural Snapshot of CYP2B4 in Complex with Paroxetine Provides Insights into Ligand Binding and Clusters of Conformational States.

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

(2013) J.Pharmacol.Exp.Ther. 346: 113-120

  • DOI: 10.1124/jpet.113.204776

  • PubMed Abstract: 
  • An X-ray crystal structure of CYP2B4 in complex with the drug paroxetine [(3S,4R)-3-[(2H-1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine] was solved at 2.14 Å resolution. The structure revealed a conformation intermediate to that of the ...

    An X-ray crystal structure of CYP2B4 in complex with the drug paroxetine [(3S,4R)-3-[(2H-1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine] was solved at 2.14 Å resolution. The structure revealed a conformation intermediate to that of the recently solved complex with amlodipine and that of the more compact complex with 4-(4-chlorophenyl)imidazole in terms of the placement of the F-G cassette. Moreover, comparison of the new structure with 15 previously solved structures of CYP2B4 revealed some new insights into the determinants of active-site size and shape. The 2B4-paroxetine structure is nearly superimposable on a previously solved closed structure in a ligand-free state. Despite the overall conformational similarity among multiple closed structures, the active-site cavity volume of the paroxetine complex is enlarged. Further analysis of the accessible space and binding pocket near the heme reveals a new subchamber that resulted from the movement of secondary structural elements and rearrangements of active-site side chains. Overall, the results from the comparison of all 16 structures of CYP2B4 demonstrate a cluster of protein conformations that were observed in the presence or absence of various ligands.


    Organizational Affiliation

    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, Mail Code 0703, La Jolla, CA 92093-0703, USA. m7shah@ucsd.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2B4
A
476Oryctolagus cuniculusMutation(s): 9 
Gene Names: CYP2B4
EC: 1.14.14.1
Find proteins for P00178 (Oryctolagus cuniculus)
Go to UniProtKB:  P00178
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CM5
Query on CM5

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A
5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE; CYMAL-5
C23 H42 O11
RVTGFZGNOSKUDA-ZNGNCRBCSA-N
 Ligand Interaction
HEM
Query on HEM

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A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
8PR
Query on 8PR

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A
Paroxetine
(3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine
C19 H20 F N O3
AHOUBRCZNHFOSL-YOEHRIQHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8PRKd: 700 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.760α = 90.00
b = 90.760β = 90.00
c = 153.681γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
SCALAdata scaling
REFMACrefinement
iMOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references