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- PDB-5sau: DDR1, 3-[2-(6-aminopyridin-3-yl)ethynyl]-N-[3-(trifluoromethyl)ph... -

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Basic information

Entry
Database: PDB / ID: 5sau
TitleDDR1, 3-[2-(6-aminopyridin-3-yl)ethynyl]-N-[3-(trifluoromethyl)phenyl]benzamide, 1.800A, P212121, Rfree=23.1%
ComponentsEpithelial discoidin domain-containing receptor 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / RTK / RECEPTOR TYROSINE KINASE / COLLAGEN / DISCOIDIN DOMAIN / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / ear development / regulation of cell-matrix adhesion / 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 / ear development / regulation of cell-matrix adhesion / 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 / receptor protein-tyrosine kinase / positive regulation of neuron projection development / protein autophosphorylation / cell population proliferation / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-1IF / MALONATE ION / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStihle, M. / Richter, H. / Benz, J. / Hochstrasser, R. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche Switzerland
CitationJournal: To be published
Title: Crystal Structure of a DDR1 complex
Authors: Richter, H. / Prunotto, M. / Kuhn, B. / Rudolph, M.G.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,9863
Polymers36,5031
Non-polymers4832
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.514, 74.156, 75.105
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Epithelial discoidin domain-containing receptor 1 / Epithelial discoidin domain receptor 1 / CD167 antigen-like family member A / Cell adhesion kinase ...Epithelial discoidin domain receptor 1 / CD167 antigen-like family member A / Cell adhesion kinase / Discoidin receptor tyrosine kinase / HGK2 / Mammary carcinoma kinase 10 / MCK-10 / Protein-tyrosine kinase 3A / Protein-tyrosine kinase RTK-6 / TRK E / Tyrosine kinase DDR / Tyrosine-protein kinase CAK


Mass: 36502.855 Da / Num. of mol.: 1 / Fragment: tyrosine kinase domain, residues 593-913 / Mutation: Deletion of residues 730-735
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE / Plasmid: pFastBac1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q08345, receptor protein-tyrosine kinase
#2: Chemical ChemComp-1IF / 3-[(6-aminopyridin-3-yl)ethynyl]-N-[3-(trifluoromethyl)phenyl]benzamide


Mass: 381.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H14F3N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 7.6 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed with reservoir consisting of 0.1M MES/NaOH pH 6.5, 0.2M KI, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.05 Å / Num. obs: 33027 / % possible obs: 99.7 % / Redundancy: 6.48 % / Biso Wilson estimate: 36.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.086 / Χ2: 0.982 / Net I/σ(I): 11.61 / Num. measured all: 214006 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.855.7092.0890.813246240823200.3272.29896.3
1.85-1.96.741.7541.1415785234923420.5341.999.7
1.9-1.956.7521.2081.6915502229622960.6161.309100
1.95-2.016.6530.8162.4614756221922180.8310.885100
2.01-2.086.3690.5383.5913795216921660.8950.58699.9
2.08-2.156.4170.3575.1813366208420830.950.389100
2.15-2.236.820.2956.313721201420120.9640.31999.9
2.23-2.326.7620.2457.5513185195119500.9720.26599.9
2.32-2.436.6210.16210.2912414187518750.9870.176100
2.43-2.546.3040.12912.1611171177317720.9890.14199.9
2.54-2.686.610.10314.6711356171917180.9930.11299.9
2.68-2.846.7470.08418.110950162316230.9950.091100
2.84-3.046.6440.07220.2910132152515250.9960.078100
3.04-3.286.2530.0623.318979143714360.9970.06699.9
3.28-3.66.4770.05426.688563132213220.9980.059100
3.6-4.026.5940.05428.477893119711970.9980.058100
4.02-4.656.1770.04930.196684108310820.9970.05499.9
4.65-5.696.110.04829.4756279229210.9980.05299.9
5.69-8.056.1950.0529.7445357327320.9980.054100
8.05-48.055.3680.05529.6323464454370.9960.06198.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_4230refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.8→48.05 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1674 5.08 %RANDOM
Rwork0.1991 31269 --
obs0.2008 32943 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.75 Å2 / Biso mean: 41.8181 Å2 / Biso min: 22.23 Å2
Refinement stepCycle: final / Resolution: 1.8→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 35 178 2509
Biso mean--32.7 41.77 -
Num. residues----287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.850.48131250.50822527265298
1.85-1.910.46361330.448825742707100
1.91-1.980.37121490.31225592708100
1.98-2.060.3021330.246225822715100
2.06-2.150.26711340.221425932727100
2.15-2.270.30771300.238325802710100
2.27-2.410.27841220.219426082730100
2.41-2.60.22841490.200125842733100
2.6-2.860.22961290.19826462775100
2.86-3.270.24541540.20525972751100
3.27-4.120.19061540.173526522806100
4.12-48.050.19251620.158827672929100

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