5MHP | pdb_00005mhp

Novel Imidazo[1,2-a]pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.245 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5MHP

Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Discovery of 2-[[2-Ethyl-6-[4-[2-(3-hydroxyazetidin-1-yl)-2-oxoethyl]piperazin-1-yl]-8-methylimidazo[1,2-a]pyridin-3-yl]methylamino]-4-(4-fluorophenyl)thiazole-5-carbonitrile (GLPG1690), a First-in-Class Autotaxin Inhibitor Undergoing Clinical Evaluation for the Treatment of Idiopathic Pulmonary Fibrosis.

Desroy, N.Housseman, C.Bock, X.Joncour, A.Bienvenu, N.Cherel, L.Labeguere, V.Rondet, E.Peixoto, C.Grassot, J.M.Picolet, O.Annoot, D.Triballeau, N.Monjardet, A.Wakselman, E.Roncoroni, V.Le Tallec, S.Blanque, R.Cottereaux, C.Vandervoort, N.Christophe, T.Mollat, P.Lamers, M.Auberval, M.Hrvacic, B.Ralic, J.Oste, L.van der Aar, E.Brys, R.Heckmann, B.

(2017) J Med Chem 60: 3580-3590

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00032
  • Primary Citation Related Structures: 
    5MHP

  • PubMed Abstract: 

    Autotaxin is a circulating enzyme with a major role in the production of lysophosphatic acid (LPA) species in blood. A role for the autotaxin/LPA axis has been suggested in many disease areas including pulmonary fibrosis. Structural modifications of the known autotaxin inhibitor lead compound 1, to attenuate hERG inhibition, remove CYP3A4 time-dependent inhibition, and improve pharmacokinetic properties, led to the identification of clinical candidate GLPG1690 (11). Compound 11 was able to cause a sustained reduction of LPA levels in plasma in vivo and was shown to be efficacious in a bleomycin-induced pulmonary fibrosis model in mice and in reducing extracellular matrix deposition in the lung while also reducing LPA 18:2 content in bronchoalveolar lavage fluid. Compound 11 is currently being evaluated in an exploratory phase 2a study in idiopathic pulmonary fibrosis patients.


  • Organizational Affiliation
    • Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France.

Macromolecule Content 

  • Total Structure Weight: 102.85 kDa 
  • Atom Count: 6,390 
  • Modeled Residue Count: 768 
  • Deposited Residue Count: 871 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2871Homo sapiensMutation(s): 1 
Gene Names: ENPP2ATXPDNP2
EC: 3.1.4.39 (PDB Primary Data), 3.1.4.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13822 (Homo sapiens)
Explore Q13822 
Go to UniProtKB:  Q13822
PHAROS:  Q13822
GTEx:  ENSG00000136960 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13822
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q13822-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G91845HM
GlyCosmos: G91845HM
GlyGen: G91845HM

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7NB

Query on 7NB



Download:Ideal Coordinates CCD File
O [auth A]2-[[2-ethyl-8-methyl-6-[4-[2-(3-oxidanylazetidin-1-yl)-2-oxidanylidene-ethyl]piperazin-1-yl]imidazo[1,2-a]pyridin-3-yl]-methyl-amino]-4-(4-fluorophenyl)-1,3-thiazole-5-carbonitrile
C30 H33 F N8 O2 S
REQQVBGILUTQNN-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
H [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
PO4

Query on PO4



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN

Query on SCN



Download:Ideal Coordinates CCD File
L [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
7NB BindingDB:  5MHP Ki: 15 (nM) from 1 assay(s)
IC50: min: 1.00e-2, max: 100 (nM) from 11 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.23α = 90
b = 79.53β = 100.78
c = 79.74γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data 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: 2017-08-30
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary