5K0I

mpges1 bound to an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.159 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.146 (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 6PWClick 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

Characterization of 3,3-dimethyl substituted N-aryl piperidines as potent microsomal prostaglandin E synthase-1 inhibitors.

Kuklish, S.L.Antonysamy, S.Bhattachar, S.N.Chandrasekhar, S.Fisher, M.J.Fretland, A.J.Gooding, K.Harvey, A.Hughes, N.E.Luz, J.G.Manninen, P.R.McGee, J.E.Navarro, A.Norman, B.H.Partridge, K.M.Quimby, S.J.Schiffler, M.A.Sloan, A.V.Warshawsky, A.M.York, J.S.Yu, X.P.

(2016) Bioorg Med Chem Lett 26: 4824-4828

  • DOI: https://doi.org/10.1016/j.bmcl.2016.08.023
  • Primary Citation of Related Structures:  
    5K0I

  • PubMed Abstract: 

    Here we report on novel, potent 3,3-dimethyl substituted N-aryl piperidine inhibitors of microsomal prostaglandin E synthases-1(mPGES-1). Example 14 potently inhibited PGE2 synthesis in an ex vivo human whole blood (HWB) assay with an IC50 of 7nM. In addition, 14 had no activity in human COX-1 or COX-2 assays at 30μM, and failed to inhibit human mPGES-2 at 62.5μM in a microsomal prep assay. These data are consistent with selective mPGES-1-mediated reduction of PGE2. In dog, 14 had oral bioavailability (74%), clearance (3.62mL/(min*kg)) and volume of distribution (Vd,ss=1.6L/kg) values within our target ranges. For these reasons, 14 was selected for further study.


  • Organizational Affiliation

    Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, IN 46285, USA. Electronic address: Kuklish_Steven@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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6PW
Query on 6PW

Download Ideal Coordinates CCD File 
B [auth A]1,5-anhydro-2,3,4-trideoxy-3-{[(4S)-3,3-dimethyl-1-(8-methylquinolin-2-yl)piperidine-4-carbonyl]amino}-D-erythro-hexitol
C24 H33 N3 O3
OLJFTJILJDDJGV-SLFFLAALSA-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],
G [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
6PW BindingDB:  5K0I IC50: min: 2, max: 23 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.159 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.444α = 90
b = 77.444β = 90
c = 123.565γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

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 6PWClick on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view detailsBest fitted BOGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary