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- PDB-7feh: Crystal structure of human DDR1 in complex with CH5541127 -

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Basic information

Entry
Database: PDB / ID: 7feh
TitleCrystal structure of human DDR1 in complex with CH5541127
ComponentsEpithelial discoidin domain-containing receptor 1
KeywordsTRANSFERASE / RECEPTOR TYROSINE KINASE / COLLAGEN / DISCOIDIN DOMAIN
Function / homology
Function and homology information


protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension ...protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension / axon development / Non-integrin membrane-ECM interactions / mammary gland alveolus development / peptidyl-tyrosine autophosphorylation / collagen binding / lactation / embryo implantation / transmembrane receptor protein tyrosine kinase activity / regulation of cell growth / cell surface receptor protein tyrosine kinase signaling pathway / receptor protein-tyrosine kinase / positive regulation of neuron projection development / cell population proliferation / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell adhesion / negative regulation of cell population proliferation / extracellular space / extracellular exosome / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Galactose-binding-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-3UI / NITRATE ION / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsFukami, T.A. / Kadono, S. / Matsuura, T.
CitationJournal: Medicinal Chemistry Research / Year: 2023
Title: Novel potent and highly selective DDR1 inhibitors from integrated lead finding
Authors: 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.
History
DepositionJul 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epithelial discoidin domain-containing receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8414
Polymers36,2111
Non-polymers6303
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint1 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.390, 61.700, 63.110
Angle α, β, γ (deg.)90.000, 106.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Epithelial discoidin domain-containing receptor 1


Mass: 36210.656 Da / Num. of mol.: 1 / Fragment: Residues: 593-913
Source method: isolated from a genetically manipulated source
Details: del:730-735 / Source: (gene. exp.) Homo sapiens (human) / Gene: DDR1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q08345, receptor protein-tyrosine kinase
#2: Chemical ChemComp-3UI / N-[(5-chloranyl-2-ethylsulfonyl-phenyl)methyl]-3-piperazin-1-yl-5-(trifluoromethyloxy)benzamide


Mass: 505.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23ClF3N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.01 % / Mosaicity: 0 °
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 10 mg/mL protein, 1 mM Ligand, 2 %(v/v) DMSO, 21.0 %(w/v) PEG 2000 MME, 0.25 M NaNO3, 0.1 M BIS-TRIS propane (pH 6.6), 5.0 %(v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→38.782 Å / Num. obs: 38162 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.9 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Rsym value: 0.052 / Net I/av σ(I): 7.6 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.61-1.663.40.41.827900.2550.4760.4100
1.66-1.73.50.3292.227530.2040.3880.32999.7
1.7-1.753.40.2582.827000.1610.3050.25899.6
1.75-1.83.40.213.425570.1320.2480.2199.8
1.8-1.863.30.174.225270.1090.2020.1799.8
1.86-1.933.10.1325.424200.0890.160.13299.7
1.93-23.40.1066.723320.0670.1260.10699.1
2-2.083.40.088822390.0550.1040.08899
2.08-2.183.40.0759.221720.0470.0890.07599
2.18-2.283.30.06510.420420.0420.0770.06599.1
2.28-2.413.20.05711.519950.0380.0690.05799.6
2.41-2.553.30.05112.418720.0330.0610.05199.2
2.55-2.733.50.04913.117460.030.0580.04999.5
2.73-2.953.50.04413.616370.0280.0520.04499.7
2.95-3.233.40.04313.815030.0270.0510.04399.4
3.23-3.613.10.04114.113660.0280.050.04199.6
3.61-4.173.50.03913.812120.0250.0460.03999.6
4.17-5.13.50.03814.810440.0240.0450.03899.8
5.1-7.223.10.03713.38010.0240.0440.03799.7
7.22-38.7823.50.03216.84540.020.0380.03298.9

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.24data extraction
xia20.3.1.6data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→38.78 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2057 1909 5 %
Rwork0.1655 36234 -
obs0.1676 38143 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.04 Å2 / Biso mean: 24.9512 Å2 / Biso min: 9.75 Å2
Refinement stepCycle: final / Resolution: 1.61→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 41 226 2595
Biso mean--26.1 33.68 -
Num. residues----293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.61-1.650.26621370.21152546100
1.65-1.70.21831260.19292616100
1.7-1.750.21221230.1811260599
1.75-1.810.24561350.17822545100
1.81-1.870.23831250.17922608100
1.87-1.940.24051260.17922602100
1.94-2.030.21411350.1578258199
2.03-2.140.19961370.1575254799
2.14-2.270.20411210.1616259299
2.27-2.450.21191370.1635258599
2.45-2.70.21071370.1718259399
2.7-3.090.20441590.16662593100
3.09-3.890.1911550.1504257599
3.89-38.780.19251560.16432646100

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