5SAU | pdb_00005sau

DDR1, 3-[2-(6-aminopyridin-3-yl)ethynyl]-N-[3-(trifluoromethyl)phenyl]benzamide, 1.800A, P212121, Rfree=23.1%

PDB DOI: https://doi.org/10.2210/pdb5SAU/pdb
Deposition Group: G_1002213 | Explore G_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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.231 (Depositor), 0.234 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.201 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of a DDR1 complex

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

To be published.

Macromolecule Content

Total Structure Weight: 36.99 kDa
Atom Count: 2,517
Modeled Residue Count: 287
Deposited Residue Count: 321
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08345
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1IF (Subject of Investigation/LOI) Query on 1IF Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3-[(6-aminopyridin-3-yl)ethynyl]-N-[3-(trifluoromethyl)phenyl]benzamide C₂₁ H₁₄ F₃ N₃ O MWTXIEKNSGTHCF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.231 (Depositor), 0.234 (DCC)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.514	α = 90
b = 74.156	β = 90
c = 75.105	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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-29

Deposition Author(s):

Hochstrasser, R.

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

Revision History (Full details and data files)

Version 1.0: 2022-06-29
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.