6W35 | pdb_00006w35

A new Autotaxin Inhibitor for the Treatment of Idiopathic Pulmonary Fibrosis: A Clinical Candidate Discovered Using DNA-Encoded Chemistry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.230 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

Literature

Novel Autotaxin Inhibitor for the Treatment of Idiopathic Pulmonary Fibrosis: A Clinical Candidate Discovered Using DNA-Encoded Chemistry.

Cuozzo, J.W.Clark, M.A.Keefe, A.D.Kohlmann, A.Mulvihill, M.Ni, H.Renzetti, L.M.Resnicow, D.I.Ruebsam, F.Sigel, E.A.Thomson, H.A.Wang, C.Xie, Z.Zhang, Y.

(2020) J Med Chem 63: 7840-7856

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00688
  • Primary Citation Related Structures: 
    6W35

  • PubMed Abstract: 

    The activity of the secreted phosphodiesterase autotaxin produces the inflammatory signaling molecule LPA and has been associated with a number of human diseases including idiopathic pulmonary fibrosis (IPF). We screened a single DNA-encoded chemical library (DECL) of 225 million compounds and identified a series of potent inhibitors. Optimization of this series led to the discovery of compound 1 (X-165), a highly potent, selective, and bioavailable small molecule. Cocrystallization of compound 1 with human autotaxin demonstrated that it has a novel binding mode occupying both the hydrophobic pocket and a channel near the autotaxin active site. Compound 1 inhibited the production of LPA in human and mouse plasma at nanomolar levels and showed efficacy in a mouse model of human lung fibrosis. After successfully completing IND-enabling studies, compound 1 was approved by the FDA for a Phase I clinical trial. These results demonstrate that DECL hits can be readily optimized into clinical candidates.


  • Organizational Affiliation
    • X-Chem, Inc., 100 Beaver Street, Suite 101, Waltham, Massachusetts 02543, United States.

Macromolecule Content 

  • Total Structure Weight: 97.77 kDa 
  • Atom Count: 7,099 
  • Modeled Residue Count: 792 
  • Deposited Residue Count: 818 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ectonucleotide pyrophosphatase/phosphodiesterase 2818Pan troglodytesMutation(s): 4 
Gene Names: ENPP2
EC: 3.1.4.4 (UniProt), 3.1.4.39 (UniProt)
UniProt
Find proteins for K7CID1 (Pan troglodytes)
Explore K7CID1 
Go to UniProtKB:  K7CID1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7CID1
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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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 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SKV
(Subject of Investigation/LOI)

Query on SKV



Download:Ideal Coordinates CCD File
D [auth A]2-fluoranyl-~{N}-[(2~{R})-1-[1-(2~{H}-indazol-5-yl)-3-methyl-2,4-bis(oxidanylidene)-1,3,8-triazaspiro[4.5]decan-8-yl]-3-methyl-1-oxidanylidene-butan-2-yl]-5-(trifluoromethyl)benzamide
C28 H28 F4 N6 O4
CDSKRHGFXHZEQL-JOCHJYFZSA-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
BA [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
ZN

Query on ZN



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

Query on SCN



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

Query on CA



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

Query on CL



Download:Ideal Coordinates CCD File
CA [auth A]
DA [auth A]
L [auth A]
M [auth A]
N [auth A]
CA [auth A],
DA [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.230 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.723α = 90
b = 77.377β = 112.11
c = 94.433γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-07-08 
  • Deposition Author(s): Cuozzo, J.W.

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-08-05
    Changes: Database references
  • Version 2.2: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
  • Version 2.3: 2024-10-16
    Changes: Structure summary