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- PDB-6fiq: DDR1, 1-(1H-indazole-5-carbonyl)-5'-methoxy-1'-[2-oxo-2-[(2S)-2-(... -

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Basic information

Entry
Database: PDB / ID: 6fiq
TitleDDR1, 1-(1H-indazole-5-carbonyl)-5'-methoxy-1'-[2-oxo-2-[(2S)-2-(trifluoromethyl)pyrrolidin-1-yl]ethyl]spiro[piperidine-4,3'-pyrrolo[3,2-b]pyridine]-2'-one, 1.790A, P212121, Rfree=23.8%
ComponentsEpithelial discoidin domain-containing receptor 1
KeywordsTRANSFERASE / RTK / RECEPTOR TYROSINE KINASE / COLLAGEN / DISCOIDIN DOMAIN
Function / homology
Function and homology information


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 / neuron projection extension / smooth muscle cell migration / axon development ...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 / neuron projection extension / smooth muscle cell migration / axon development / Non-integrin membrane-ECM interactions / mammary gland alveolus development / peptidyl-tyrosine autophosphorylation / collagen binding / transmembrane receptor protein tyrosine kinase activity / lactation / embryo implantation / regulation of cell growth / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / GPI-linked ephrin receptor activity / transmembrane-ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / positive regulation of neuron projection development / cell surface receptor protein tyrosine kinase signaling pathway / protein autophosphorylation / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-DJW / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,0953
Polymers36,5031
Non-polymers5922
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.934, 71.668, 72.644
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)
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-DJW / 1-(1~{H}-indazol-5-ylcarbonyl)-5'-methoxy-1'-[2-oxidanylidene-2-[(2~{S})-2-(trifluoromethyl)pyrrolidin-1-yl]ethyl]spiro[piperidine-4,3'-pyrrolo[3,2-b]pyridine]-2'-one


Mass: 556.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27F3N6O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
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: Sep 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.999981
211
ReflectionResolution: 1.79→46.23 Å / Num. obs: 30156 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.24 % / Biso Wilson estimate: 34.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.103 / Rsym value: 0.086 / Χ2: 0.988 / Net I/σ(I): 10.08 / Num. measured all: 217022
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 7.03 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 0.74 / Num. measured obs: 2564 / Num. possible: 411 / Num. unique obs: 406 / CC1/2: 0.999 / Rrim(I) all: 0.037 / Rsym value: 0.949 / Rejects: 0 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_2067refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.79→46.231 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1530 5.09 %random
Rwork0.199 28507 --
obs0.2011 30037 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.88 Å2 / Biso mean: 40.7955 Å2 / Biso min: 22.01 Å2
Refinement stepCycle: final / Resolution: 1.79→46.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 41 150 2536
Biso mean--34.3 42.89 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072443
X-RAY DIFFRACTIONf_angle_d1.0133314
X-RAY DIFFRACTIONf_chiral_restr0.048354
X-RAY DIFFRACTIONf_plane_restr0.005456
X-RAY DIFFRACTIONf_dihedral_angle_d14.7591490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.79-1.84780.41691420.42222489263198
1.8478-1.91380.39331250.3552552267799
1.9138-1.99050.33321310.295225652696100
1.9905-2.0810.33191170.25125822699100
2.081-2.19080.27711320.231325762708100
2.1908-2.3280.25191310.212625772708100
2.328-2.50770.22731580.206325682726100
2.5077-2.76010.24861560.20925912747100
2.7601-3.15940.25611320.210226072739100
3.1594-3.98020.21751490.172726392788100
3.9802-46.2460.20151570.164927612918100

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