6HP9 | pdb_00006hp9

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

• PDB DOI: https://doi.org/10.2210/pdb6HP9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-09-19 Released: 2019-01-30 
• Deposition Author(s): Pinkas, D.M., Fox, A.E., Kupinska, K., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 31310125 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00365
• Primary Citation Related Structures: 
  6HP9


• 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.

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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.
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , 190 Kaiyuan Avenue , Guangzhou 510530 , China.
Division of Surgical Oncology, Department of Surgery and Hamon Center for Therapeutic Oncology Research , UT Southwestern , Dallas , Texas 75390-8593 , United States.
Structural Genomics Consortium , University of Oxford , Old Road Campus Research Building, Roosevelt Drive , Oxford OX3 7DQ , U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.47 kDa 
• Atom Count: 5,041 
• Modeled Residue Count: 578 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epithelial discoidin domain-containing receptor 1	A, B	315	Homo sapiens	Mutation(s): 0  Gene Names: DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q08345 (Homo sapiens) Explore Q08345  Go to UniProtKB:  Q08345
PHAROS:  Q08345 GTEx:  ENSG00000204580

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GKB (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2~{R})-~{N}-[3-(4-methylimidazol-1-yl)-5-(trifluoromethyl)phenyl]-2-(pyrimidin-5-ylamino)-2,3-dihydro-1~{H}-indene-5-carboxamide C25 H21 F3 N6 O XFLAQLCDMJRPFH-HXUWFJFHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.51	α = 90
b = 65.89	β = 90
c = 162.88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Pinkas, D.M., Fox, A.E., Kupinska, K., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N., Structural Genomics Consortium (SGC)

Revision History  

• 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