DDR1, 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-N-methylacetamide, 1.440A, P1211, Rfree=24.1%

Experimental Data Snapshot

  • Resolution: 1.44 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


DNA-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in a Genetic Mouse Model of Alport Syndrome.

Richter, H.Satz, A.L.Bedoucha, M.Buettelmann, B.Petersen, A.C.Harmeier, A.Hermosilla, R.Hochstrasser, R.Burger, D.Gsell, B.Gasser, R.Huber, S.Hug, M.N.Kocer, B.Kuhn, B.Ritter, M.Rudolph, M.G.Weibel, F.Molina-David, J.Kim, J.J.Santos, J.V.Stihle, M.Georges, G.J.Bonfil, R.D.Fridman, R.Uhles, S.Moll, S.Faul, C.Fornoni, A.Prunotto, M.

(2019) ACS Chem Biol 14: 37-49

  • DOI: https://doi.org/10.1021/acschembio.8b00866
  • Primary Citation of Related Structures:  
    6FER, 6FEW, 6FEX, 6FIL, 6FIN, 6FIO, 6FIQ

  • PubMed Abstract: 

    The importance of Discoidin Domain Receptor 1 (DDR1) in renal fibrosis has been shown via gene knockout and use of antisense oligonucleotides; however, these techniques act via a reduction of DDR1 protein, while we prove the therapeutic potential of inhibiting DDR1 phosphorylation with a small molecule. To date, efforts to generate a selective small-molecule to specifically modulate the activity of DDR1 in an in vivo model have been unsuccessful. We performed parallel DNA encoded library screens against DDR1 and DDR2, and discovered a chemical series that is highly selective for DDR1 over DDR2. Structure-guided optimization efforts yielded the potent DDR1 inhibitor 2.45, which possesses excellent kinome selectivity (including 64-fold selectivity over DDR2 in a biochemical assay), a clean in vitro safety profile, and favorable pharmacokinetic and physicochemical properties. As desired, compound 2.45 modulates DDR1 phosphorylation in vitro as well as prevents collagen-induced activation of renal epithelial cells expressing DDR1. Compound 2.45 preserves renal function and reduces tissue damage in Col4a3 -/- mice (the preclinical mouse model of Alport syndrome) when employing a therapeutic dosing regime, indicating the real therapeutic value of selectively inhibiting DDR1 phosphorylation in vivo. Our results may have wider significance as Col4a3 -/- mice also represent a model for chronic kidney disease, a disease which affects 10% of the global population.

  • Organizational Affiliation

    Roche Pharma Research and Early Development, Roche Innovation Center , Basel 4070 , Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epithelial discoidin domain-containing receptor 1321Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q08345 (Homo sapiens)
Explore Q08345 
Go to UniProtKB:  Q08345
PHAROS:  Q08345
GTEx:  ENSG00000204580 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08345
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on D6W

Download Ideal Coordinates CCD File 
B [auth A]2-[8-(2~{H}-indazol-5-ylcarbonyl)-4-oxidanylidene-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-~{N}-methyl-ethanamide
C24 H26 N6 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
D6W Binding MOAD:  6FEW IC50: 1410 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.44 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.58α = 90
b = 62.051β = 106.58
c = 63.419γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description