5FDX | pdb_00005fdx

Structure of DDR1 receptor tyrosine kinase in complex with D2164 inhibitor at 2.65 Angstroms resolution.

• PDB DOI: https://doi.org/10.2210/pdb5FDX/pdb

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


• Deposited: 2015-12-16 Released: 2016-10-26 
• Deposition Author(s): Bartual, S.G., Pinkas, D.M., Wang, Z., Ding, K., Mahajan, P., Kupinska, K., Mukhopadhyay, S., Strain-Damerell, C., Chalk, R., Borkowska, O., Talon, R., Kopec, J., Williams, E., Tallant, C., Chaikuad, A., Sorell, F., Newman, J., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.273 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of DDR1 receptor tyrosine kinase in complex with D2164 inhibitor at 2.65 Angstroms resolution.

Bartual, S.G., Ding, K., Wang, Z., Bullock, N.A.

To be published.

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: 78.24 kDa 
• Atom Count: 4,569 
• Modeled Residue Count: 554 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epithelial discoidin domain-containing receptor 1	A, B	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
5X1	C [auth A], I [auth B]	3-[(4-methylpiperazin-1-yl)methyl]-~{N}-[(4~{R})-4-methyl-2-pyrimidin-5-yl-3,4-dihydro-1~{H}-isoquinolin-7-yl]-5-(trifluoromethyl)benzamide C28 H31 F3 N6 O FXWGWJNBGHQODS-IBGZPJMESA-N
PEG	H [auth A], K [auth B], L [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5X1	BindingDB:  5FDX	IC50: min: 66.2, max: 76 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.273 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.548	α = 90
b = 120.34	β = 94.87
c = 63.02	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: 2016-10-26 
Deposition Author(s): Bartual, S.G., Pinkas, D.M., Wang, Z., Ding, K., Mahajan, P., Kupinska, K., Mukhopadhyay, S., Strain-Damerell, C., Chalk, R., Borkowska, O., Talon, R., Kopec, J., Williams, E., Tallant, C., Chaikuad, A., Sorell, F., Newman, J., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Structure summary
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary