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- PDB-7bcm: The DDR1 Kinase Domain Bound To SR302 -

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Basic information

Entry
Database: PDB / ID: 7bcm
TitleThe DDR1 Kinase Domain Bound To SR302
ComponentsEpithelial discoidin domain-containing receptor 1
KeywordsTRANSFERASE / Kinase Cancer Inhibitor
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-TBK / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMathea, S. / Chatterjee, D. / Preuss, F. / Roehm, S. / Joerger, A. / Knapp, S.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Development of a Selective Dual Discoidin Domain Receptor (DDR)/p38 Kinase Chemical Probe.
Authors: Rohm, S. / Berger, B.T. / Schroder, M. / Chatterjee, D. / Mathea, S. / Joerger, A.C. / Pinkas, D.M. / Bufton, J.C. / Tjaden, A. / Kovooru, L. / Kudolo, M. / Pohl, C. / Bullock, A.N. / ...Authors: Rohm, S. / Berger, B.T. / Schroder, M. / Chatterjee, D. / Mathea, S. / Joerger, A.C. / Pinkas, D.M. / Bufton, J.C. / Tjaden, A. / Kovooru, L. / Kudolo, M. / Pohl, C. / Bullock, A.N. / Muller, S. / Laufer, S. / Knapp, S.
History
DepositionDec 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,7544
Polymers71,5082
Non-polymers1,2462
Water37821
1
A: Epithelial discoidin domain-containing receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3772
Polymers35,7541
Non-polymers6231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epithelial discoidin domain-containing receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3772
Polymers35,7541
Non-polymers6231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.223, 120.402, 62.095
Angle α, β, γ (deg.)90.000, 111.348, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 35754.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q08345, receptor protein-tyrosine kinase
#2: Chemical ChemComp-TBK / ~{N}-[[4-[[(2~{S})-4-cyclohexyl-1-[[(3~{S})-1-methylsulfonylpiperidin-3-yl]amino]-1-oxidanylidene-butan-2-yl]carbamoyl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide


Mass: 622.778 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H42N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG10,000 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→41.71 Å / Num. obs: 33763 / % possible obs: 98.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 32.31 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3333

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Processing

Software
NameVersionClassification
REFMAC7.0.053refinement
PHENIX1.18.2_3874refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BKJ

4bkj


Resolution: 2.3→41.71 Å / SU ML: 0.3942 / Cross valid method: FREE R-VALUE / σ(F): 1.61 / Phase error: 31.3547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.308 1701 5.04 %
Rwork0.243 32055 -
obs0.2462 33756 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.79 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 88 21 4281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154361
X-RAY DIFFRACTIONf_angle_d1.51145928
X-RAY DIFFRACTIONf_chiral_restr0.0704659
X-RAY DIFFRACTIONf_plane_restr0.0096801
X-RAY DIFFRACTIONf_dihedral_angle_d24.9439670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.40471390.30032676X-RAY DIFFRACTION99.68
2.37-2.440.36341300.27622694X-RAY DIFFRACTION99.68
2.44-2.530.36811500.26962664X-RAY DIFFRACTION99.58
2.53-2.630.2851430.26412671X-RAY DIFFRACTION99.36
2.63-2.750.32891420.25952664X-RAY DIFFRACTION98.32
2.75-2.90.35251490.2512579X-RAY DIFFRACTION96.33
2.9-3.080.32811410.262672X-RAY DIFFRACTION98.98
3.08-3.320.32791510.25522681X-RAY DIFFRACTION99.4
3.32-3.650.28961540.24352674X-RAY DIFFRACTION99.05
3.65-4.180.25161450.22032678X-RAY DIFFRACTION98.71
4.18-5.260.28281330.21292688X-RAY DIFFRACTION99.09
5.26-41.710.31881240.23642714X-RAY DIFFRACTION97.83

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