Structure of the kinase domain of human DDR1 in complex with a potent and selective inhibitor of DDR1 and DDR2

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Design, Synthesis, and Biological Evaluation of 3-(Imidazo[1,2- a]pyrazin-3-ylethynyl)-4-isopropyl- N-(3-((4-methylpiperazin-1-yl)methyl)-5-(trifluoromethyl)phenyl)benzamide as a Dual Inhibitor of Discoidin Domain Receptors 1 and 2.

Wang, Z.Zhang, Y.Pinkas, D.M.Fox, A.E.Luo, J.Huang, H.Cui, S.Xiang, Q.Xu, T.Xun, Q.Zhu, D.Tu, Z.Ren, X.Brekken, R.A.Bullock, A.N.Liang, G.Ding, K.Lu, X.

(2018) J Med Chem 61: 7977-7990

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01045
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Discoidin-domain receptors 1 and 2 (DDR1 and DDR2) are new potential targets for anti-inflammatory-drug discovery. A series of heterocycloalkynylbenzimides were designed and optimized to coinhibit DDR1 and DDR2. One of the most promising compounds, 5n, tightly bound to DDR1 and DDR2 proteins with K d values of 7.9 and 8.0 nM; potently inhibited the kinases with IC 50 values of 9.4 and 20.4 nM, respectively; and was significantly less potent for a panel of 403 wild-type kinases at 1.0 μM. DDR1- and DDR2-kinase inhibition by 5n was validated by Western-blotting analysis in primary human lung fibroblasts. The compound also dose-dependently inhibited lipopolysaccharide (LPS)-induced interleukin 6 (IL-6) release in vitro and exhibited promising in vivo anti-inflammatory effects in an LPS-induced-acute-lung-injury (ALI) mouse model. Compound 5n may serve as a lead compound for new anti-inflammatory drug discovery.

  • Organizational Affiliation

    International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FEW (Subject of Investigation/LOI)
Query on FEW

Download Ideal Coordinates CCD File 
C [auth A],
R [auth B]
C31 H31 F3 N6 O
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
S [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
S [auth B],
T [auth B]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
FEW Binding MOAD:  6GWR Kd: 7.9 (nM) from 1 assay(s)
BindingDB:  6GWR Kd: 7.9 (nM) from 1 assay(s)
IC50: 9.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.2α = 90
b = 118.75β = 92.05
c = 61.43γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata 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: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-29
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2018-09-26
    Changes: Data collection, Database references