4YL1

Crystal Structures of mPGES-1 Inhibitor Complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 
    0.175 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4U8Click on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view detailsBest fitted BOGClick on this verticalbar to view details

This is version 1.4 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: https://doi.org/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. 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 Biotechnology Center San Diego, 10300 Campus Point Drive, Suite 200, San Diego, California 92121, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prostaglandin E synthase148Homo sapiensMutation(s): 0 
Gene Names: PTGESMGST1L1MPGES1PGESPIG12
EC: 5.3.99.3 (PDB Primary Data), 1.11.1 (UniProt), 2.5.1.18 (UniProt)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O14684 (Homo sapiens)
Explore O14684 
Go to UniProtKB:  O14684
PHAROS:  O14684
GTEx:  ENSG00000148344 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14684
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4U8
Query on 4U8

Download Ideal Coordinates CCD File 
B [auth A]5-(4-tert-butylphenyl)-1-[4-(propan-2-yloxy)phenyl]-1H-indole-2-carboxylic acid
C28 H29 N O3
GUMCVDVWBMLUSQ-UHFFFAOYSA-N
GSH
Query on GSH

Download Ideal Coordinates CCD File 
D [auth A]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
BOG
Query on BOG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
G [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
4U8 BindingDB:  4YL1 IC50: min: 62, max: 2580 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free:  0.175 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.585α = 90
b = 76.585β = 90
c = 123.617γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing
Cootmodel building
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4U8Click on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view detailsBest fitted BOGClick on this verticalbar to view details

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: Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Structure summary