3NTG

Crystal structure of COX-2 with selective compound 23d-(R)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The novel benzopyran class of selective cyclooxygenase-2 inhibitors. Part 2: The second clinical candidate having a shorter and favorable human half-life.

Wang, J.L.Limburg, D.Graneto, M.J.Springer, J.Hamper, J.R.Liao, S.Pawlitz, J.L.Kurumbail, R.G.Maziasz, T.Talley, J.J.Kiefer, J.R.Carter, J.

(2010) Bioorg.Med.Chem.Lett. 20: 7159-7163

  • DOI: 10.1016/j.bmcl.2010.07.054
  • Primary Citation of Related Structures:  3LN0, 3LN1, 3MQE

  • PubMed Abstract: 
  • In this Letter, we provide the structure-activity relationships, optimization of design, testing criteria, and human half-life data for a series of selective COX-2 inhibitors. During the course of our structure-based drug design efforts, we discovere ...

    In this Letter, we provide the structure-activity relationships, optimization of design, testing criteria, and human half-life data for a series of selective COX-2 inhibitors. During the course of our structure-based drug design efforts, we discovered two distinct binding modes within the COX-2 active site for differently substituted members of this class. The challenge of a undesirably long human half-life for the first clinical candidate 1t(1/2)=360 h was addressed by multiple strategies, leading to the discovery of 29b-(S) (SC-75416) with t(1/2)=34 h.


    Organizational Affiliation

    Pfizer Global Research and Development, Chesterfield, MO 63017, USA. jl47wang@yahoo.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin G/H synthase 2
A, B, C, D
552Mus musculusGene Names: Ptgs2 (Cox-2, Cox2, Pghs-b, Tis10)
EC: 1.14.99.1
Find proteins for Q05769 (Mus musculus)
Go to UniProtKB:  Q05769
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D72
Query on D72

Download SDF File 
Download CCD File 
A, B, C, D
(2R)-6,8-dichloro-7-(2-methylpropoxy)-2-(trifluoromethyl)-2H-chromene-3-carboxylic acid
C15 H13 Cl2 F3 O4
FQKMILFVTQADHR-CYBMUJFWSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
A, D
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D72IC50: <28 nM (88) BINDINGDB
D72IC50: 28 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 180.268α = 90.00
b = 134.273β = 90.00
c = 122.615γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance