3N8X

Crystal Structure of Cyclooxygenase-1 in Complex with Nimesulide

Structural Biology Knowledgebase: 3N8X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.181

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3N8X

Classification: OXIDOREDUCTASE

Total Structure Weight: 132510.42

Macromolecule Entities
Molecule Chains Length Organism Details
Prostaglandin G/H synthase 1 A, B 553 Ovis aries EC#: 1.14.99.1 IUBMB
Mutation: M92L
Gene Name(s): PTGS1 Gene View COX1

Membrane Protein

Source: mpstruc | 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

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

A, B 4-NITRO-2-PHENOXYMETHANESULFONANILIDE
NIMESULIDE (Synonym)
C13 H12 N2 O5 S
HYWYRSMBCFDLJT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BOG
Query on BOG

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

A 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 %)
NIM IC50: 3760 - 59000 nM (93 - 99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.181
  • Space Group: P 65
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 181.71 α = 90.00
b = 181.71 β = 90.00
c = 103.45 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-05-28
  • Released Date: 2010-07-28
  • Deposition author(s): Lee, J.Y.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4