5FDP | pdb_00005fdp

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

• PDB DOI: https://doi.org/10.2210/pdb5FDP/pdb

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


• Deposited: 2015-12-16 Released: 2016-06-08 
• Deposition Author(s): Bartual, S.G., Pinkas, D.M., Wang, Z., Ding, K., Mahajan, P., Kupinska, K., Mukhopadhyay, S., Strain-Damerell, C., Borkowska, O., Talon, R., Kopec, J., Williams, E., Tallant, C., Chaikuad, A., Sorell, F., Newman, J., Burgess-Brown, N., Arrowsmith, C.H., von Delft, F., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

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

• PubMed: 27219676 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b00140
• Primary Citation of Related Structures:  
  5FDP


• 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 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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.22 kDa 
• Atom Count: 2,603 
• Modelled Residue Count: 285 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epithelial discoidin domain-containing receptor 1	A	337	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5WR	B [auth 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
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5WR	BindingDB:  5FDP	IC50: min: 21, max: 38 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.3	α = 90
b = 63.15	β = 90
c = 107.67	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): Bartual, S.G., Pinkas, D.M., Wang, Z., Ding, K., Mahajan, P., Kupinska, K., Mukhopadhyay, S., Strain-Damerell, C., Borkowska, O., Talon, R., Kopec, J., Williams, E., Tallant, C., Chaikuad, A., Sorell, F., Newman, J., Burgess-Brown, N., Arrowsmith, C.H., von Delft, F., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description