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- PDB-6fio: DDR1, 2-[1'-(1H-indazole-5-carbonyl)-4-methyl-2-oxospiro[indole-3... -

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Basic information

Entry
Database: PDB / ID: 6fio
TitleDDR1, 2-[1'-(1H-indazole-5-carbonyl)-4-methyl-2-oxospiro[indole-3,4'-piperidine]-1-yl]-N-(2,2,2-trifluoroethyl)acetamide, 1.990A, P6522, Rfree=27.7%
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-DJH / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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)37,0022
Polymers36,5031
Non-polymers4991
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.908, 111.908, 113.288
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1225-

HOH

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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-DJH / 2-[1'-(1~{H}-indazol-5-ylcarbonyl)-4-methyl-2-oxidanylidene-spiro[indole-3,4'-piperidine]-1-yl]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide


Mass: 499.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24F3N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.8 Å3/Da / Density % sol: 56.15 %
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: 0.97949 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
211
ReflectionResolution: 1.99→48.46 Å / Num. obs: 29121 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 19.09 % / Biso Wilson estimate: 35.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.236 / Rrim(I) all: 0.327 / Rsym value: 0.236 / Χ2: 0.946 / Net I/σ(I): 8.65 / Num. measured all: 557871
Reflection shellResolution: 1.99→2.09 Å / Redundancy: 18.38 % / Rmerge(I) obs: 1.062 / Mean I/σ(I) obs: 0.47 / Num. measured obs: 6673 / Num. possible: 418 / Num. unique obs: 411 / CC1/2: 1 / Rrim(I) all: 0.029 / Rsym value: 1.062 / Rejects: 0 / % possible all: 98.6

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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: 1.99→48.458 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 1451 5.05 %random
Rwork0.2137 27307 --
obs0.217 28758 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.92 Å2 / Biso mean: 54.9566 Å2 / Biso min: 25.13 Å2
Refinement stepCycle: final / Resolution: 1.99→48.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 36 128 2622
Biso mean--37.77 48.42 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072563
X-RAY DIFFRACTIONf_angle_d1.0073478
X-RAY DIFFRACTIONf_chiral_restr0.043371
X-RAY DIFFRACTIONf_plane_restr0.004481
X-RAY DIFFRACTIONf_dihedral_angle_d16.3041564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.06120.41371280.42162490261892
2.0612-2.14370.40591190.3672692281198
2.1437-2.24120.36511330.33342678281198
2.2412-2.35940.40141540.33752673282799
2.3594-2.50720.36621540.26322709286399
2.5072-2.70080.28691340.25312744287899
2.7008-2.97250.33191510.22662736288799
2.9725-3.40260.27931400.211727972937100
3.4026-4.28650.26031630.16528032966100
4.2865-48.47190.19771750.15429853160100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.79851.21673.00994.4789-1.47456.6187-0.21020.5312-0.1183-0.3811-0.0168-0.1594-0.0247-0.33030.19490.50860.05630.08380.5759-0.15050.3131-12.486529.5137-25.1302
23.73843.2567-3.10313.2732-1.37746.622-0.6431.49871.3125-1.12130.17550.9693-1.5619-0.04740.54321.25960.0029-0.18030.8760.10860.7267-12.747243.5246-30.4523
36.64694.1918-0.81649.7551-1.03074.1278-0.17540.1046-1.3464-0.25640.0926-0.38090.584-0.36110.08840.4616-0.0553-0.01370.494-0.03890.444-20.823822.8066-21.1316
43.5101-1.1503-0.26132.8585-0.54853.769-0.18690.5054-0.3579-0.53230.15870.0475-0.17230.13460.00050.367-0.05390.04210.4719-0.04610.2847-17.727833.8131-20.9319
57.8301-1.8525-3.25587.4544-0.28243.859-0.2004-0.71360.60450.42190.3791-1.1736-0.2530.7818-0.18650.3775-0.0753-0.02180.4856-0.03070.4811-4.003145.60411.3812
61.2972-0.0680.10411.0942-0.29642.73340.0062-0.002-0.0130.0123-0.0382-0.0395-0.0395-0.12730.03710.2585-0.0292-0.00410.2516-0.00420.2361-21.864833.15783.7481
78.4786-0.39321.09777.95060.08442.0356-0.2645-0.53280.8495-0.0733-0.19160.4505-1.1283-0.22660.49060.58470.1085-0.03950.38110.01610.3511-26.296350.26362.3355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 598 through 629 )A598 - 629
2X-RAY DIFFRACTION2chain 'A' and (resid 630 through 650 )A630 - 650
3X-RAY DIFFRACTION3chain 'A' and (resid 651 through 678 )A651 - 678
4X-RAY DIFFRACTION4chain 'A' and (resid 679 through 708 )A679 - 708
5X-RAY DIFFRACTION5chain 'A' and (resid 709 through 733 )A709 - 733
6X-RAY DIFFRACTION6chain 'A' and (resid 734 through 891 )A734 - 891
7X-RAY DIFFRACTION7chain 'A' and (resid 892 through 906 )A892 - 906

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