3LN0

Structure of compound 5c-S bound at the active site of COX-2

Structural Biology Knowledgebase: 3LN0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.209

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3LN0

Classification: OXIDOREDUCTASE

Total Structure Weight: 277916.53

Macromolecule Entities
Molecule Chains Length Organism Details
Prostaglandin G/H synthase 2 A, B, C, D 587 Mus musculus EC#: 1.14.99.1 IUBMB
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 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A, B, C, D PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
52B
Query on 52B

A, B, C, D (2S)-6,8-dichloro-2-(trifluoromethyl)-2H- chromene-3-carboxylic acid
C11 H5 Cl2 F3 O3
ZFKBWSREWJOSSJ-VIFPVBQESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BOG
Query on BOG

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

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
52B IC50: 9.8 - 10 nM (87) BindingDB

IC50: 10 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.209
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 181.01 α = 90.00
b = 135.20 β = 90.00
c = 124.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-02-01
  • Released Date: 2010-10-27
  • Deposition author(s): Kiefer, J.R., Kurumbail, R.G., Stallings, W.C., Pawlitz, J.L.

Revision History

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