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- PDB-6few: 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: 6few
TitleDDR1, 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-N-methylacetamide, 1.440A, P1211, Rfree=24.1%
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 / cell surface receptor protein tyrosine kinase signaling pathway / 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 / transmembrane-ephrin receptor activity / GPI-linked 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 / 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 / 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-D6W / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 3, 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)36,9492
Polymers36,5031
Non-polymers4471
Water4,684260
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 area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.580, 62.051, 63.419
Angle α, β, γ (deg.)90.000, 106.580, 90.000
Int Tables number4
Space group name H-MP1211

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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
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 11.5 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed 3:1 in 600 nL with 0.1M Ca acetate, 12% PEG 8K, 0.1M Na cacodylate pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→43.42 Å / Num. obs: 53860 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.26 % / Biso Wilson estimate: 16.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.066 / Rsym value: 0.058 / Χ2: 1.024 / Net I/σ(I): 9.34
Reflection shellResolution: 1.44→1.53 Å / Redundancy: 3.36 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 0.65 / Num. unique obs: 694 / CC1/2: 1 / Rrim(I) all: 0.015 / Rsym value: 0.847 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1803refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.44→43.42 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 2705 5.09 %random
Rwork0.2171 50390 --
obs0.2184 53095 97.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.04 Å2 / Biso mean: 31.1001 Å2 / Biso min: 9.89 Å2
Refinement stepCycle: final / Resolution: 1.44→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 33 260 2631
Biso mean--22.65 35.54 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072447
X-RAY DIFFRACTIONf_angle_d1.0893314
X-RAY DIFFRACTIONf_chiral_restr0.075355
X-RAY DIFFRACTIONf_plane_restr0.005451
X-RAY DIFFRACTIONf_dihedral_angle_d12.804947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.44-1.46620.38231300.3862672280299
1.4662-1.49440.51161260.5042357248387
1.4944-1.52490.39291480.36812709285799
1.5249-1.55810.33031230.32632733285699
1.5581-1.59430.3241420.313727012843100
1.5943-1.63420.33031580.280727172875100
1.6342-1.67840.28061360.245227012837100
1.6784-1.72780.27061380.221127242862100
1.7278-1.78350.24861400.226426932833100
1.7835-1.84730.23421510.22952738288999
1.8473-1.92120.45351230.40172400252388
1.9212-2.00870.31821490.26852517266693
2.0087-2.11460.23961530.205827262879100
2.1146-2.2470.26911400.23462489262992
2.247-2.42050.25261330.22912505263893
2.4205-2.66410.24731370.196627552892100
2.6641-3.04950.19611600.194227242884100
3.0495-3.84170.22641680.175527222890100
3.8417-43.44060.15441500.151528072957100
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)
10.3563-0.2873-0.62052.09271.26112.23340.1693-0.21390.08520.3342-0.16540.1293-0.0555-0.24280.03710.3438-0.02880.05660.2723-0.02560.1999-8.4651-8.976624.6584
20.93730.2379-0.13021.815-0.40391.56540.0016-0.05770.03480.0485-0.0326-0.03960.02570.04730.02930.09380.0001-0.00630.118-0.01380.12585.91610.83185.6641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 603 through 678 )A603 - 678
2X-RAY DIFFRACTION2chain 'A' and (resid 679 through 911 )A679 - 911

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