5FDP

Structure of DDR1 receptor tyrosine kinase in complex with D2099 inhibitor at 2.25 Angstroms resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Design of Tetrahydroisoquinoline-7-carboxamides as Selective Discoidin Domain Receptor 1 (DDR1) Inhibitors.

Wang, Z.Bian, H.Bartual, S.G.Du, W.Luo, J.Zhao, H.Zhang, S.Mo, C.Zhou, Y.Xu, Y.Tu, Z.Ren, X.Lu, X.Brekken, R.A.Yao, L.Bullock, A.N.Su, J.Ding, K.

(2016) J.Med.Chem. 59: 5911-5916

  • DOI: 10.1021/acs.jmedchem.6b00140

  • PubMed Abstract: 
  • The structure-based design of 1, 2, 3, 4-tetrahydroisoquinoline derivatives as selective DDR1 inhibitors is reported. One of the representative compounds, 6j, binds to DDR1 with a Kd value of 4.7 nM and suppresses its kinase activity with an IC50 val ...

    The structure-based design of 1, 2, 3, 4-tetrahydroisoquinoline derivatives as selective DDR1 inhibitors is reported. One of the representative compounds, 6j, binds to DDR1 with a Kd value of 4.7 nM and suppresses its kinase activity with an IC50 value of 9.4 nM, but it is significantly less potent for a panel of 400 nonmutated kinases. 6j also demonstrated reasonable pharmacokinetic properties and a promising oral therapeutic effect in a bleomycin-induced mouse pulmonary fibrosis model.


    Organizational Affiliation

    State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , 190 Kaiyuan Avenue, Guangzhou 510530, China.,Department of Biochemistry and Molecular Biology, The Fourth Military Medical University , 17 Changle Western Road, Xi'an, Shaanxi 710032, P. R. China.,University of the Chinese Academy of Sciences , 19 Yuquan Road, Beijing 100049, China.,Structural Genomics Consortium, University of Oxford , Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K.,School of Pharmacy, Jinan University , 601 Huangpu Avenue West, Guangzhou 510632, China.,Division of Surgical Oncology, Department of Surgery and the Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center , Dallas Texas 75390-8593, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epithelial discoidin domain-containing receptor 1
A
337Homo sapiensMutation(s): 0 
Gene Names: DDR1 (CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE)
EC: 2.7.10.1
Find proteins for Q08345 (Homo sapiens)
Go to Gene View: DDR1
Go to UniProtKB:  Q08345
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
5WR
Query on 5WR

Download SDF File 
Download CCD File 
A
(4~{S})-4-methyl-~{N}-[3-[(4-methylpiperazin-1-yl)methyl]-5-(trifluoromethyl)phenyl]-2-pyrimidin-5-yl-3,4-dihydro-1~{H}-isoquinoline-7-carboxamide
C28 H31 F3 N6 O
YXESXLYKZKCWFJ-LJQANCHMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5WRIC50: 309 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.300α = 90.00
b = 63.150β = 90.00
c = 107.670γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Structure summary