5BQI | pdb_00005bqi

Discovery of a Potent and Selective mPGES-1 Inhibitor for the Treatment of Pain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.181 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.165 (Depositor) 
  • R-Value Observed: 
    0.165 (Depositor) 

wwPDB Validation 3D Report Full Report

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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: 18.99 kDa 
  • Atom Count: 1,392 
  • 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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4UL

Query on 4UL



Download:Ideal Coordinates CCD File
B [auth A]2-(difluoromethyl)-5-{[(2-methylpropanoyl)amino]methyl}-N-{5-methyl-4-[4-(trifluoromethyl)phenyl]-1H-imidazol-2-yl}pyridine-3-carboxamide
C23 H22 F5 N5 O2
BZYSILFNUIGABU-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
D [auth A],
E [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
F [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
1KA

Query on 1KA



Download:Ideal Coordinates CCD File
G [auth A](2-hydroxyethoxy)acetaldehyde
C4 H8 O3
DSGGHBUAHUMMHN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.181 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.165 (Depositor) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.335α = 90
b = 76.335β = 90
c = 123.561γ = 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