3QMO

X-ray crystal structure of NS-398 bound to the cyclooxygenase channel of cyclooxygenase-2

Structural Biology Knowledgebase: 3QMO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.176

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QMO

Classification: OXIDOREDUCTASE

Total Structure Weight: 144947.78

Macromolecule Entities
Molecule Chains Length Organism Details
Prostaglandin G/H synthase 2 A, B 610 Mus musculus EC#: 1.14.99.1 IUBMB
Mutation: N594A
Gene Name(s): Ptgs2 Cox-2 Cox2 Pghs-b Tis10

Membrane Protein

Source: inferred by homology | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Cyclooxygenases

Protein Name: Cyclooxygenase-2


Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BMA
Query on BMA

B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
JSmol
BOG
Query on BOG

A B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
Ligand Explorer
 
JSmol
GOL
Query on GOL

A, B GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
HEM
Query on HEM

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

B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
JSmol
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
JSmol
NDG
Query on NDG

A, B 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
JSmol
NS4
Query on NS4

A, B N-[2-(cyclohexyloxy)-4-nitrophenyl]methanesulfonamide
C13 H18 N2 O5 S
KTDZCOWXCWUPEO-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NS4 IC50: 1 - 3200 nM (86 - 98) BindingDB
Ki: 42 - 920 nM (86) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.176
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 120.43 α = 90.00
b = 131.21 β = 90.00
c = 179.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-02-04
  • Released Date: 2011-08-03
  • Deposition author(s): Vecchio, A.J., Malkowski, M.G.

Revision History

  • 2011-10-19
    Type: Citation | Details: Citation update page numbers
  • 2011-09-28
    Type: Citation | Details: Citation update
  • 2011-08-24
    Type: Citation | Details: Update citation