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

Literature

Macromolecules
Sequence Display for 4PH9

Classification: OXIDOREDUCTASE

Total Structure Weight: 132709.63

Macromolecule Entities
Molecule Chains Length Organism Details
Prostaglandin G/H synthase 2 A, B 551 Mus musculus EC#: 1.14.99.1 IUBMB
Fragment: UNP residues 20-568
Gene Name(s): Ptgs2 Cox-2 Cox2 Pghs-b Tis10
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Cyclooxygenases

Protein Name: Cyclooxygenase-2


Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A, B PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BOG
Query on BOG

A, B B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IBP
Query on IBP

A, B IBUPROFEN
2-(4-ISOBUTYLPHENYL)PROPIONIC ACID (Synonym)
C13 H18 O2
HEFNNWSXXWATRW-JTQLQIEISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AKR
Query on AKR

A, B ACRYLIC ACID
C3 H4 O2
NIXOWILDQLNWCW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IBP IC50: 730 - 265500 nM (87 - 88) BindingDB

N/A in BindingMoad
N/A in PDBbind

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 = 120.94 α = 90.00
b = 132.23 β = 90.00
c = 180.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-05-05
  • Released Date: 2014-11-26
  • Deposition author(s): Orlando, B.J., Lucido, M.J., Malkowski, M.G.

Revision History

  • 2014-12-17
    Type: Database references
  • 2015-01-07
    Type: Database references
  • 2015-02-25
    Type: Derived calculations
  • 2017-09-06
    Type: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary