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- PDB-6fil: DDR1, 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazasp... -

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Basic information

Entry
Database: PDB / ID: 6fil
TitleDDR1, 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-N-methylacetamide, 1.730A, P212121, Rfree=24.5%
ComponentsEpithelial discoidin domain-containing receptor 1
KeywordsTRANSFERASE / RTK / 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 / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-D6W / IODIDE ION / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsStihle, M. / Richter, H. / Benz, J. / Kuhn, B. / Rudolph, M.G.
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: DNA-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in a Genetic Mouse Model of Alport Syndrome.
Authors: Richter, H. / Satz, A.L. / Bedoucha, M. / Buettelmann, B. / Petersen, A.C. / Harmeier, A. / Hermosilla, R. / Hochstrasser, R. / Burger, D. / Gsell, B. / Gasser, R. / Huber, S. / Hug, M.N. / ...Authors: Richter, H. / Satz, A.L. / Bedoucha, M. / Buettelmann, B. / Petersen, A.C. / Harmeier, A. / Hermosilla, R. / Hochstrasser, R. / Burger, D. / Gsell, B. / Gasser, R. / Huber, S. / Hug, M.N. / Kocer, B. / Kuhn, B. / Ritter, M. / Rudolph, M.G. / Weibel, F. / Molina-David, J. / Kim, J.J. / Santos, J.V. / Stihle, M. / Georges, G.J. / Bonfil, R.D. / Fridman, R. / Uhles, S. / Moll, S. / Faul, C. / Fornoni, A. / Prunotto, M.
History
DepositionJan 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)37,0763
Polymers36,5031
Non-polymers5732
Water4,540252
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-0 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.042, 74.750, 75.080
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: DEL(730-735) 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-N-methylacetamide
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-D6W / 2-[8-(2~{H}-indazol-5-ylcarbonyl)-4-oxidanylidene-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-~{N}-methyl-ethanamide


Mass: 446.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N6O3
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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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: 5.5
Details: 11.3 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed 1.3:1 with 90mM MES/NaOH pH6.5, 0.18M potassium iodide, 0.2M Li2SO4, 22.5% PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.999981
211
ReflectionResolution: 1.73→47.83 Å / Num. obs: 34598 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 5.74 % / Biso Wilson estimate: 22.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.098 / Rsym value: 0.087 / Χ2: 1.017 / Net I/σ(I): 11.27 / Num. measured all: 226174
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 6.53 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.1 / Num. measured obs: 2887 / Num. possible: 495 / Num. unique obs: 491 / CC1/2: 1 / Rrim(I) all: 0.023 / Rsym value: 0.832 / Rejects: 0 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1730refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.73→47.826 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 1722 5.04 %random
Rwork0.1924 32475 --
obs0.195 34197 92.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.38 Å2 / Biso mean: 34.3751 Å2 / Biso min: 14.85 Å2
Refinement stepCycle: final / Resolution: 1.73→47.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 34 252 2582
Biso mean--25.28 40.96 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072474
X-RAY DIFFRACTIONf_angle_d1.0713361
X-RAY DIFFRACTIONf_chiral_restr0.042355
X-RAY DIFFRACTIONf_plane_restr0.005463
X-RAY DIFFRACTIONf_dihedral_angle_d12.556982
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.73-1.78090.32921400.31532875301599
1.7809-1.83840.34841570.30862871302899
1.8384-1.90410.39081350.36342542267788
1.9041-1.98040.4124980.33891806190462
1.9804-2.07050.27851560.22522878303499
2.0705-2.17970.23741550.196528683023100
2.1797-2.31620.2959920.21731794188661
2.3162-2.4950.19781330.175329533086100
2.495-2.74610.26071650.182729113076100
2.7461-3.14340.23471580.180829723130100
3.1434-3.96010.21411610.17092892305397
3.9601-47.84420.21971720.157231133285100
Refinement TLS params.Method: refined / Origin x: 18.1866 Å / Origin y: -10.8496 Å / Origin z: -4.9188 Å
111213212223313233
T0.1795 Å20.038 Å20.0136 Å2-0.1937 Å20.0184 Å2--0.1814 Å2
L1.1278 °20.203 °20.4228 °2-1.1167 °20.1457 °2--1.2313 °2
S-0.0051 Å °-0.0624 Å °-0.004 Å °-0.0456 Å °0.0012 Å °0.0083 Å °-0.1214 Å °-0.0764 Å °0.0093 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA604 - 906
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 236
5X-RAY DIFFRACTION1allS237
6X-RAY DIFFRACTION1allS238
7X-RAY DIFFRACTION1allS239 - 246
8X-RAY DIFFRACTION1allS247 - 252

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