5BQG | pdb_00005bqg

Crystal Structure of mPGES-1 Bound to an Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.169 (Depositor), 0.168 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5BQG

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery and Characterization of 2-Acylaminoimidazole Microsomal Prostaglandin E Synthase-1 Inhibitors.

Schiffler, M.A.Antonysamy, S.Bhattachar, S.N.Campanale, K.M.Chandrasekhar, S.Condon, B.Desai, P.V.Fisher, M.J.Groshong, C.Harvey, A.Hickey, M.J.Hughes, N.E.Jones, S.A.Kim, E.J.Kuklish, S.L.Luz, J.G.Norman, B.H.Rathmell, R.E.Rizzo, J.R.Seng, T.W.Thibodeaux, S.J.Woods, T.A.York, J.S.Yu, X.P.

(2016) J Med Chem 59: 194-205

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01249
  • Primary Citation Related Structures: 
    5BQG, 5BQH, 5BQI

  • PubMed Abstract: 

    As part of a program aimed at the discovery of antinociceptive therapy for inflammatory conditions, a screening hit was found to inhibit microsomal prostaglandin E synthase-1 (mPGES-1) with an IC50 of 17.4 μM. Structural information was used to improve enzyme potency by over 1000-fold. Addition of an appropriate substituent alleviated time-dependent cytochrome P450 3A4 (CYP3A4) inhibition. Further structure-activity relationship (SAR) studies led to 8, which had desirable potency (IC50 = 12 nM in an ex vivo human whole blood (HWB) assay) and absorption, distribution, metabolism, and excretion (ADME) properties. Studies on the formulation of 8 identified 8·H3PO4 as suitable for clinical development. Omission of a lipophilic portion of the compound led to 26, a readily orally bioavailable inhibitor with potency in HWB comparable to celecoxib. Furthermore, 26 was selective for mPGES-1 inhibition versus other mechanisms in the prostanoid pathway. These factors led to the selection of 26 as a second clinical candidate.


  • Organizational Affiliation
    • Lilly Research Laboratories, A Division of Eli Lilly and Company , Indianapolis, Indiana 46285, United States.

Macromolecule Content 

  • Total Structure Weight: 18.74 kDa 
  • Atom Count: 1,432 
  • Modeled Residue Count: 148 
  • Deposited Residue Count: 154 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4UJ

Query on 4UJ



Download:Ideal Coordinates CCD File
B [auth A]2-chloro-N-(4-phenyl-1,3-thiazol-2-yl)benzamide
C16 H11 Cl N2 O S
FXJFKYBQUTVGOL-UHFFFAOYSA-N
GSH

Query on GSH



Download:Ideal Coordinates CCD File
C [auth A]Glutathione
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
BOG

Query on BOG



Download:Ideal Coordinates CCD File
E [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
JZR

Query on JZR



Download:Ideal Coordinates CCD File
D [auth A]hexyl beta-D-glucopyranoside
C12 H24 O6
JVAZJLFFSJARQM-RMPHRYRLSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
F [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free:  0.169 (Depositor), 0.168 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.472α = 90
b = 77.472β = 90
c = 123.123γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Structure summary