7FEH | pdb_00007feh

Crystal structure of human DDR1 in complex with CH5541127

PDB DOI: https://doi.org/10.2210/pdb7FEH/pdb

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

Deposited: 2021-07-20 Released: 2022-07-27
Deposition Author(s): Fukami, T.A., Kadono, S., Matsuura, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.206 (Depositor), 0.207 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7FEH

Ligand Structure Quality Assessment

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

Literature

Novel potent and highly selective DDR1 inhibitors from integrated lead finding

Kuhn, B., Ritter, M., Benz, J., Kocer, B., Sarie, J.C., Hochstrasser, R., Rudolph, M.G., Kadono, S., Matsuura, T., Murata, T., Richter, H., Prunotto, M.

(2023) Medicinal Chemistry Research 32: 1400-1425

DOI: https://doi.org/10.1007/s00044-023-03066-2

Macromolecule Content

Total Structure Weight: 36.84 kDa
Atom Count: 2,609
Modeled Residue Count: 293
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epithelial discoidin domain-containing receptor 1	A	320	Homo sapiens	Mutation(s): 0 Gene Names: DDR1 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
3UI (Subject of Investigation/LOI) Query on 3UI 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]	N-[(5-chloranyl-2-ethylsulfonyl-phenyl)methyl]-3-piperazin-1-yl-5-(trifluoromethyloxy)benzamide C₂₁ H₂₃ Cl F₃ N₃ O₄ S FNPFZOPPAGELAN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3UI	BindingDB: 7FEH	IC50: 84 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.206 (Depositor), 0.207 (DCC)
R-Value Work: 0.166 (Depositor), 0.166 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.39	α = 90
b = 61.7	β = 106.22
c = 63.11	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-07-27
Type: Initial release
Version 1.1: 2023-08-09
Changes: Database references
Version 1.2: 2024-05-29
Changes: Data collection

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.