5SAV | pdb_00005sav

DDR1, N-[2-[3-(2-aminopyrimidin-5-yl)oxyphenyl]ethyl]-3-(trifluoromethoxy)benzamide, 1.760A, P212121, Rfree=23.5%

• PDB DOI: https://doi.org/10.2210/pdb5SAV/pdb
• Deposition Group: G_1002213 ExploreG_1002213

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


• Deposited: 2021-06-22 Released: 2022-06-29 
• Deposition Author(s): Stihle, M., Richter, H., Benz, J., Hochstrasser, R., Rudolph, M.G.
• Funding Organization(s): F. Hoffmann-La Roche

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: other

Literature

Crystal Structure of a DDR1 complex

Richter, H., Prunotto, M., Kuhn, B., Rudolph, M.G.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.3 kDa 
• Atom Count: 2,666 
• Modeled Residue Count: 291 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epithelial discoidin domain-containing receptor 1	A	321	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1IJ (Subject of Investigation/LOI)	B [auth A]	N-(2-{3-[(2-aminopyrimidin-5-yl)oxy]phenyl}ethyl)-3-(trifluoromethoxy)benzamide C20 H17 F3 N4 O3 JABJAPNNNDHTEK-UHFFFAOYSA-N
IOD	C [auth A], D [auth A], E [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44	α = 90
b = 62.56	β = 90
c = 109.28	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Stihle, M., Richter, H., Benz, J., Hochstrasser, R., Rudolph, M.G.

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Funding Organization	Location	Grant Number
F. Hoffmann-La Roche	Switzerland	--

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description