2OYU

Indomethacin-(S)-alpha-ethyl-ethanolamide bound to Cyclooxygenase-1

Structural Biology Knowledgebase: 2OYU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.292
  • R-Value Work: 0.241

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2OYU

Classification: OXIDOREDUCTASE

Total Structure Weight: 71917.21

Macromolecule Entities
Molecule Chains Length Organism Details
Prostaglandin G/H synthase 1 P 600 Ovis aries EC#: 1.14.99.1 IUBMB
Mutation: M92L
Gene Name(s): PTGS1 Gene View COX1

Membrane Protein

Source: inferred by homology | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Cyclooxygenases

Protein Name: Ram Prostaglandin H2 synthase-1 (cyclooxygenase-1 or COX-1)


Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

P PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMS
Query on IMS

P 2-[1-(4-CHLOROBENZOYL)-5-METHOXY-2-METHYL- 1H-INDOL-3-YL]-N-[(1S)-1-(HYDROXYMETHYL)PROPYL]ACETAMIDE
C23 H25 Cl N2 O4
GKJWXEORYGBJFS-KRWDZBQOSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BOG
Query on BOG

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

P N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

P BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IMS IC50: 350 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.292
  • R-Value Work: 0.241
  • Space Group: P 65 2 2

Unit Cell:

Length (Å) Angle (°)
a = 181.41 α = 90.00
b = 181.41 β = 90.00
c = 103.40 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-23
  • Released Date: 2007-07-24
  • Deposition author(s): Harman, C.A., Garavito, R.M.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4