4YK5

Crystal Structures of mPGES-1 Inhibitor Complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of mPGES-1 Inhibitor Complexes Form a Basis for the Rational Design of Potent Analgesic and Anti-Inflammatory Therapeutics.

Luz, J.G.Antonysamy, S.Kuklish, S.L.Condon, B.Lee, M.R.Allison, D.Yu, X.P.Chandrasekhar, S.Backer, R.Zhang, A.Russell, M.Chang, S.S.Harvey, A.Sloan, A.V.Fisher, M.J.

(2015) J Med Chem 58: 4727-4737

  • DOI: 10.1021/acs.jmedchem.5b00330
  • Primary Citation of Related Structures:  
    4YK5, 4YL0, 4YL1, 4YL3

  • PubMed Abstract: 
  • Microsomal prostaglandin E synthase 1 (mPGES-1) is an α-helical homotrimeric integral membrane inducible enzyme that catalyzes the formation of prostaglandin E2 (PGE2) from prostaglandin H2 (PGH2). Inhibition of mPGES-1 has been proposed as a therapeutic strategy for the treatment of pain, inflammation, and some cancers ...

    Microsomal prostaglandin E synthase 1 (mPGES-1) is an α-helical homotrimeric integral membrane inducible enzyme that catalyzes the formation of prostaglandin E2 (PGE2) from prostaglandin H2 (PGH2). Inhibition of mPGES-1 has been proposed as a therapeutic strategy for the treatment of pain, inflammation, and some cancers. Interest in mPGES-1 inhibition can, in part, be attributed to the potential circumvention of cardiovascular risks associated with anti-inflammatory cyclooxygenase 2 inhibitors (coxibs) by targeting the prostaglandin pathway downstream of PGH2 synthesis and avoiding suppression of antithrombotic prostacyclin production. We determined the crystal structure of mPGES-1 bound to four potent inhibitors in order to understand their structure-activity relationships and provide a framework for the rational design of improved molecules. In addition, we developed a light-scattering-based thermal stability assay to identify molecules for crystallographic studies.


    Organizational Affiliation

    ‡Lilly Research Laboratories, Lilly Corporate Center, 355 East Merrill Street, Indianapolis, Indiana 46285, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Prostaglandin E synthase A154Homo sapiensMutation(s): 0 
Gene Names: PTGESMGST1L1MPGES1PGESPIG12
EC: 5.3.99.3 (PDB Primary Data), 1.11.1 (UniProt), 2.5.1.18 (UniProt)
Find proteins for O14684 (Homo sapiens)
Explore O14684 
Go to UniProtKB:  O14684
NIH Common Fund Data Resources
PHAROS:  O14684
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4DV
Query on 4DV

Download Ideal Coordinates CCD File 
A
3-[1-(4-chlorobenzyl)-5-(2-fluoro-2'-methylbiphenyl-4-yl)-3-methyl-1H-indol-2-yl]-2,2-dimethylpropanoic acid
C34 H31 Cl F N O2
IYCJVTFMIQICDJ-UHFFFAOYSA-N
 Ligand Interaction
GSH
Query on GSH

Download Ideal Coordinates CCD File 
A
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
BOG
Query on BOG

Download Ideal Coordinates CCD File 
A
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
JZR
Query on JZR

Download Ideal Coordinates CCD File 
A
hexyl beta-D-glucopyranoside
C12 H24 O6
JVAZJLFFSJARQM-RMPHRYRLSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PG0
Query on PG0

Download Ideal Coordinates CCD File 
A
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4DVIC50:  960   nM  BindingDB
4DVIC50:  23   nM  BindingDB
4DVIC50:  3   nM  BindingDB
4DVIC50:  960   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.6α = 90
b = 76.6β = 90
c = 123.736γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary