6XKD | pdb_00006xkd

Structure of ligand-bound mouse cGAMP hydrolase ENPP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.273 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure-Aided Development of Small-Molecule Inhibitors of ENPP1, the Extracellular Phosphodiesterase of the Immunotransmitter cGAMP.

Carozza, J.A.Brown, J.A.Bohnert, V.Fernandez, D.AlSaif, Y.Mardjuki, R.E.Smith, M.Li, L.

(2020) Cell Chem Biol 27: 1347-1358.e5

  • DOI: https://doi.org/10.1016/j.chembiol.2020.07.007
  • Primary Citation Related Structures: 
    6XKD

  • PubMed Abstract: 

    Cancer cells initiate an innate immune response by synthesizing and exporting the small-molecule immunotransmitter cGAMP, which activates the anti-cancer Stimulator of Interferon Genes (STING) pathway in the host. An extracellular enzyme, ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1), hydrolyzes cGAMP and negatively regulates this anti-cancer immune response. Small-molecule ENPP1 inhibitors are much needed as tools to study the basic biology of extracellular cGAMP and as investigational cancer immunotherapy drugs. Here, we surveyed structure-activity relationships around a series of cell-impermeable and thus extracellular-targeting phosphonate inhibitors of ENPP1. In addition, we solved the crystal structure of an exemplary phosphonate inhibitor to elucidate the interactions that drive potency. This study yielded several best-in-class inhibitors with K i  < 2 nM and excellent physicochemical and pharmacokinetic properties. Finally, we demonstrate that an ENPP1 inhibitor delays tumor growth in a breast cancer mouse model. Together, we have developed ENPP1 inhibitors that are excellent tool compounds and potential therapeutics.


  • Organizational Affiliation
    • Department of Chemistry, Stanford University, Stanford, CA 93405, USA; Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA.

Macromolecule Content 

  • Total Structure Weight: 191.82 kDa 
  • Atom Count: 10,875 
  • Modeled Residue Count: 1,360 
  • Deposited Residue Count: 1,646 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
A, B
823Mus musculusMutation(s): 0 
Gene Names: Enpp1
EC: 3.1.4.1 (UniProt), 3.6.1.9 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06802 (Mus musculus)
Explore P06802 
Go to UniProtKB:  P06802
IMPC:  MGI:97370
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06802
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P06802-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IJE
(Subject of Investigation/LOI)

Query on IJE



Download:Ideal Coordinates CCD File
K [auth A]{2-[1-(6,7-dimethoxyquinazolin-4-yl)piperidin-4-yl]ethyl}phosphonic acid
C17 H24 N3 O5 P
SNLWMWQNJTVWKD-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
L [auth B],
M [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



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

Query on CL



Download:Ideal Coordinates CCD File
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
IJE BindingDB:  6XKD IC50: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.273 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.35α = 90
b = 102.35β = 90
c = 172.891γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary