4PH9

The structure of Ibuprofen bound to cyclooxygenase-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

The structure of ibuprofen bound to cyclooxygenase-2.

Orlando, B.J.Lucido, M.J.Malkowski, M.G.

(2015) J.Struct.Biol. 189: 62-66

  • DOI: 10.1016/j.jsb.2014.11.005

  • PubMed Abstract: 
  • The cyclooxygenases (COX-1 and COX-2) catalyze the rate-limiting step in the biosynthesis of prostaglandins, and are the pharmacological targets of non-steroidal anti-inflammatory drugs (NSAIDs) and COX-2 selective inhibitors (coxibs). Ibuprofen (IBP ...

    The cyclooxygenases (COX-1 and COX-2) catalyze the rate-limiting step in the biosynthesis of prostaglandins, and are the pharmacological targets of non-steroidal anti-inflammatory drugs (NSAIDs) and COX-2 selective inhibitors (coxibs). Ibuprofen (IBP) is one of the most commonly available over-the-counter pharmaceuticals in the world. The anti-inflammatory and analgesic properties of IBP are thought to arise from inhibition of COX-2 rather than COX-1. While an X-ray crystal structure of IBP bound to COX-1 has been solved, no such structure exists for the cognate isoform COX-2. We have determined the crystal structure of muCOX-2 with a racemic mixture of (R/S)-IBP. Our structure reveals that only the S-isomer of IBP was bound, indicating that the S-isomer possesses higher affinity for COX-2 than the R-isomer. Mutational analysis of Arg-120 and Tyr-355 at the entrance of the cyclooxygenase channel confirmed their role in binding and inhibition of COX-2 by IBP. Our results provide the first atomic level detail of the interaction between IBP and COX-2.


    Organizational Affiliation

    Department of Structural Biology, The State University of New York at Buffalo and the Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin G/H synthase 2
A, B
551Mus musculusMutation(s): 0 
Gene Names: Ptgs2 (Cox-2, Cox2, Pghs-b, Tis10)
EC: 1.14.99.1
Find proteins for Q05769 (Mus musculus)
Go to UniProtKB:  Q05769
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
IBP
Query on IBP

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Download CCD File 
A, B
IBUPROFEN
2-(4-ISOBUTYLPHENYL)PROPIONIC ACID
C13 H18 O2
HEFNNWSXXWATRW-JTQLQIEISA-N
 Ligand Interaction
AKR
Query on AKR

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A, B
ACRYLIC ACID
C3 H4 O2
NIXOWILDQLNWCW-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

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A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BOG
Query on BOG

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A, B
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IBPKi: 7200 - >10000 nM (88) BINDINGDB
IBPIC50: 100 - 370000 nM (88) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.160 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 120.941α = 90.00
b = 132.228β = 90.00
c = 180.462γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
Cootmodel building
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM077176

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-17
    Type: Database references
  • Version 1.2: 2015-01-07
    Type: Database references
  • Version 1.3: 2015-02-25
    Type: Derived calculations
  • Version 2.0: 2017-09-06
    Type: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 2.1: 2017-11-22
    Type: Refinement description