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 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 3.0 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
  • Primary Citation of Related Structures:  
    4PH9

  • 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) is one of the most commonly available over-the-counter pharmaceuticals in the world ...

    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. Electronic address: malkowski@hwi.buffalo.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Prostaglandin G/H synthase 2A, B551Mus musculusMutation(s): 0 
Gene Names: Ptgs2Cox-2Cox2Pghs-bTis10
EC: 1.14.99.1
UniProt
Find proteins for Q05769 (Mus musculus)
Explore Q05769 
Go to UniProtKB:  Q05769
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, D2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A], U [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BOG
Query on BOG

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], V [auth B]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], W [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
IBP
Query on IBP

Download Ideal Coordinates CCD File 
F [auth A], T [auth B]IBUPROFEN
C13 H18 O2
HEFNNWSXXWATRW-JTQLQIEISA-N
 Ligand Interaction
AKR
Query on AKR

Download Ideal Coordinates CCD File 
L [auth A], M [auth A], X [auth B], Y [auth B]ACRYLIC ACID
C3 H4 O2
NIXOWILDQLNWCW-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , CA [auth B] , DA [auth B] , EA [auth B] , FA [auth B] , N [auth A] , O [auth A] , 
AA [auth B],  BA [auth B],  CA [auth B],  DA [auth B],  EA [auth B],  FA [auth B],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IBPIC50:  860   nM  BindingDB
IBPIC50:  100   nM  BindingDB
IBPIC50:  600   nM  BindingDB
IBPIC50:  1350   nM  BindingDB
IBPIC50:  1400   nM  BindingDB
IBPIC50:  265500   nM  BindingDB
IBPIC50:  1080   nM  BindingDB
IBPIC50:  1100   nM  BindingDB
IBPIC50:  14500   nM  BindingDB
IBPIC50:  730   nM  BindingDB
IBPKi:  9000   nM  BindingDB
IBPKi:  10000   nM  BindingDB
IBPIC50:  8000   nM  BindingDB
IBPKi:  9900   nM  BindingDB
IBPIC50:  2000   nM  BindingDB
IBPIC50:  7200   nM  BindingDB
IBPIC50:  6200   nM  BindingDB
IBPKi:  7200   nM  BindingDB
IBPIC50:  80000   nM  BindingDB
IBPIC50:  4200   nM  BindingDB
IBPIC50:  4300   nM  BindingDB
IBPIC50:  1500   nM  BindingDB
IBPIC50:  36000   nM  BindingDB
IBPIC50:  1100   nM  BindingDB
IBPIC50:  30000   nM  BindingDB
IBPIC50:  370000   nM  BindingDB
IBPIC50:  1400   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.941α = 90
b = 132.228β = 90
c = 180.462γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM077176

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2015-01-07
    Changes: Database references
  • Version 1.3: 2015-02-25
    Changes: Derived calculations
  • Version 2.0: 2017-09-06
    Changes: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 2.1: 2017-11-22
    Changes: Refinement description
  • Version 2.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary