4YL0

Crystal Structures of mPGES-1 Inhibitor Complexes

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 A148Homo sapiensMutation(s): 0 
Gene Names: PTGES, MGST1L1, MPGES1, PGES, PIG12
EC: 5.3.99.3 (PDB Primary Data), 1.11.1 (UniProt), 2.5.1.18 (UniProt)
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Membrane-Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG)		Protein: 
Microsomal Prostaglandin E Synthase 1 with bound compound 30
Find proteins for O14684 (Homo sapiens)
Explore O14684 
Go to UniProtKB:  O14684
NIH Common Fund Data Resources
PHAROS:  O14684
GTEx:  ENSG00000148344
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4DZ
Query on 4DZ
Download Ideal Coordinates CCD File 
A
2-(9-chloro-1H-phenanthro[9,10-d]imidazol-2-yl)benzene-1,3-dicarbonitrile
C23 H11 Cl N4
BVFLHOOKHPFDCT-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
PG4
Query on PG4
Download Ideal Coordinates CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO		AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4DZIC50:  1   nM  BindingDB
4DZIC50:  76   nM  BindingDB
4DZIC50:  1360   nM  BindingDB
4DZIC50:  1300   nM  BindingDB
4DZIC50:  1590   nM  Binding MOAD
4DZIC50:  0.8999999761581421   nM  BindingDB
4DZIC50:  3   nM  BindingDB
4DZIC50:  56   nM  BindingDB
4DZIC50:  5.300000190734863   nM  BindingDB
4DZIC50:  676   nM  BindingDB
4DZIC50:  4.300000190734863   nM  BindingDB
4DZIC50:  1590   nM  BindingDB
4DZIC50:  1.899999976158142   nM  BindingDB
4DZIC50:  6   nM  BindingDB
4DZIC50:  420   nM  BindingDB
4DZIC50:  1800   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.621α = 90
b = 76.621β = 90
c = 123.092γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Advisory, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary