6VL4

Crystal Structure of mPGES-1 bound to DG-031


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-based, multi-targeted drug discovery approach to eicosanoid inhibition: Dual inhibitors of mPGES-1 and 5-lipoxygenase activating protein (FLAP).

Ho, J.D.Lee, M.R.Rauch, C.T.Aznavour, K.Park, J.S.Luz, J.G.Antonysamy, S.Condon, B.Maletic, M.Zhang, A.Hickey, M.J.Hughes, N.E.Chandrasekhar, S.Sloan, A.V.Gooding, K.Harvey, A.Yu, X.P.Kahl, S.D.Norman, B.H.

(2020) Biochim Biophys Acta Gen Subj 1865: 129800-129800

  • DOI: https://doi.org/10.1016/j.bbagen.2020.129800
  • Primary Citation of Related Structures:  
    6VGC, 6VGI, 6VL4

  • PubMed Abstract: 

    Due to the importance of both prostaglandins (PGs) and leukotrienes (LTs) as pro-inflammatory mediators, and the potential for eicosanoid shunting in the presence of pathway target inhibitors, we have investigated an approach to inhibiting the formation of both PGs and LTs as part of a multi-targeted drug discovery effort. We generated ligand-protein X-ray crystal structures of known inhibitors of microsomal prostaglandin E2 synthase-1 (mPGES-1) and the 5-Lipoxygenase Activating Protein (FLAP), with their respective proteins, to understand the overlapping pharmacophores. We subsequently used molecular modeling and structure-based drug design (SBDD) to identify hybrid structures intended to inhibit both targets. This work enabled the preparation of compounds 4 and 5, which showed potent in vitro inhibition of both targets. Our findings enhance the structural understanding of mPGES-1 and FLAP's unique ligand binding pockets and should accelerate the discovery of additional dual inhibitors for these two important integral membrane protein drug targets.


  • Organizational Affiliation

    Lilly Biotechnology Center, San Diego, CA 92121, USA. Electronic address: ho_joseph_d@lilly.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prostaglandin E synthase154Homo 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
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.417α = 90
b = 76.417β = 90
c = 123.784γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2020-12-16
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Refinement description, Structure summary