Structure of the kinase domain of human DDR1 in complex with a 2-Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-based inhibitor

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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This is version 1.3 of the entry. See complete history


2-Amino-2,3-dihydro-1H-indene-5-carboxamide-Based Discoidin Domain Receptor 1 (DDR1) Inhibitors: Design, Synthesis, and in Vivo Antipancreatic Cancer Efficacy.

Zhu, D.Huang, H.Pinkas, D.M.Luo, J.Ganguly, D.Fox, A.E.Arner, E.Xiang, Q.Tu, Z.C.Bullock, A.N.Brekken, R.A.Ding, K.Lu, X.

(2019) J Med Chem 62: 7431-7444

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00365
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A series of 2-amino-2,3-dihydro-1 H -indene-5-carboxamides were designed and synthesized as new selective discoidin domain receptor 1 (DDR1) inhibitors. One of the representative compounds, 7f , bound with DDR1 with a K d value of 5.9 nM and suppressed the kinase activity with an half-maximal (50%) inhibitory concentration value of 14.9 nM. 7f potently inhibited collagen-induced DDR1 signaling and epithelial-mesenchymal transition, dose-dependently suppressed colony formation of pancreatic cancer cells, and exhibited promising in vivo therapeutic efficacy in orthotopic mouse models of pancreatic cancer.

  • Organizational Affiliation

    International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), School of Pharmacy , Jinan University , 601 Huangpu Avenue West , Guangzhou 510632 , China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epithelial discoidin domain-containing receptor 1
A, B
315Homo 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
GKB (Subject of Investigation/LOI)
Query on GKB

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C25 H21 F3 N6 O
Binding Affinity Annotations 
IDSourceBinding Affinity
GKB Binding MOAD:  6HP9 IC50: 5.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.51α = 90
b = 65.89β = 90
c = 162.88γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description