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- PDB-7be6: Structure of DDR1 receptor tyrosine kinase in complex with inhibi... -

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Basic information

Entry
Database: PDB / ID: 7be6
TitleStructure of DDR1 receptor tyrosine kinase in complex with inhibitor SR159
ComponentsEpithelial discoidin domain-containing receptor 1
KeywordsTRANSFERASE / DDR1 receptor tyrosine kinase / kinase inhibitor / structure-based design / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein tyrosine kinase collagen receptor activity / 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 / smooth muscle cell migration / neuron projection extension ...protein tyrosine kinase collagen receptor activity / 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 / smooth muscle cell migration / neuron projection extension / axon development / Non-integrin membrane-ECM interactions / mammary gland alveolus development / peptidyl-tyrosine autophosphorylation / embryo implantation / collagen binding / lactation / transmembrane receptor protein tyrosine kinase activity / regulation of cell growth / positive regulation of neuron projection development / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / cell population proliferation / protein autophosphorylation / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Chem-TJW / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87081933411 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Roehm, S. / Joerger, A.C. / Knapp, S. / Bullock, A.N. / Structural Genomics Consortium (SGC)
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 22, 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

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)37,04311
Polymers35,7541
Non-polymers1,28910
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint21 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.023, 131.967, 43.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 1 molecules A

#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.: 1
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

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Non-polymers , 5 types, 168 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TJW / 5-amino-N-(4-(((2S)-4-cyclohexyl-1-((1-(methylsulfonyl)piperidin-3-yl)amino)-1-oxobutan-2-yl)carbamoyl)benzyl)-1-phenyl-1H-pyrazole-4-carboxamide / 5-azanyl-~{N}-[[4-[[(2~{S})-4-cyclohexyl-1-[[(3~{S})-1-methylsulfonylpiperidin-3-yl]amino]-1-oxidanylidene-butan-2-yl]carbamoyl]phenyl]methyl]-1-phenyl-pyrazole-4-carboxamide / inhibitor SR159


Mass: 663.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H45N7O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20% PEG 3350, 10% ethylene glycol, 0.1 M BisTrisPropane pH 6.5, 0.2 M sodium sulfate (50 nL protein and 100 nL reservoir)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.87→65.9835 Å / Num. obs: 31065 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 27.1840593147 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.8
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1542 / CC1/2: 0.855 / % possible all: 99.7

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fdx

5fdx


Resolution: 1.87081933411→65.9835 Å / SU ML: 0.229843049536 / Cross valid method: FREE R-VALUE / σ(F): 1.35256581224 / Phase error: 23.2630776394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.230440082701 1542 4.9737122214 %
Rwork0.186795116458 29461 -
obs0.188989674436 31003 99.9516409827 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.7961154469 Å2
Refinement stepCycle: LAST / Resolution: 1.87081933411→65.9835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 85 158 2643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007555157445522547
X-RAY DIFFRACTIONf_angle_d0.8817376759273441
X-RAY DIFFRACTIONf_chiral_restr0.0542744217007368
X-RAY DIFFRACTIONf_plane_restr0.00560820654572444
X-RAY DIFFRACTIONf_dihedral_angle_d21.65870175531521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87081933411-1.93120.3069923483781310.2683646785072633X-RAY DIFFRACTION99.8554913295
1.9312-2.00020.2701633480281470.2148063472452632X-RAY DIFFRACTION100
2.0002-2.08030.2521247614971600.198575763682615X-RAY DIFFRACTION99.8920086393
2.0803-2.1750.24693504281460.1867095183192640X-RAY DIFFRACTION99.9282639885
2.175-2.28970.2401065001361180.1867883837972648X-RAY DIFFRACTION100
2.2897-2.43310.2294870929591240.1861435356482690X-RAY DIFFRACTION100
2.4331-2.6210.2431980847681290.187420869932654X-RAY DIFFRACTION100
2.621-2.88480.2547924848471370.1871076491392677X-RAY DIFFRACTION99.9644760213
2.8848-3.30220.2198801203941480.1913851828482687X-RAY DIFFRACTION100
3.3022-4.16030.2003240346681400.1704117441662728X-RAY DIFFRACTION100
4.1603-65.98350.2285783308231620.1833389797452857X-RAY DIFFRACTION99.8346560847
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)
10.334882024432-0.32162448525-0.1119063529470.3560550632970.1688693505090.10682710166-0.260474999759-0.103173199743-0.0232139996250.1099140740420.1376433273440.3692139673650.230189308141-0.105963373077-0.02955705240630.3206896310040.0129217619850.01051454753430.278915945059-0.01913208752670.503926397187-12.70088474331.86254958408-17.9308464362
20.3365239951940.004058374540070.3006886825170.1952721389820.0851164683910.31560406397-0.0619665167666-0.0341658982683-0.2699646857380.0158524245230.0435264948308-0.003468465108180.118828826003-0.038106919652-6.27930776613E-50.224188525476-0.01564353648210.006965582055070.195744713626-0.01805749343480.27378944807-16.603574200814.1070003491-18.6641393269
30.874587446848-0.3987737638390.07995641110090.5136329173740.03576098867650.5527440381990.00650194168020.03343620990780.08694771277240.02757055025350.0147869885072-0.0612394585365-0.0107175496052-0.03572453849911.19310673415E-50.1883198123130.00480647827473-0.00313378755790.203303619666-0.0127036511390.160108198579-22.200943367732.5653558131-16.7118421329
40.8155083838210.0766528376307-0.04057009708540.214655968497-0.209323566410.250998557309-0.041857190486-0.2807145227430.238195392380.3377799235980.08718592331930.0870590695686-0.0499358167339-0.1235020194190.03735793104550.3044818062620.0274420954707-0.01037041228630.264976548662-0.05367079976570.16531834063-22.697704979135.786269964-2.79263863018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 600 through 650 )
2X-RAY DIFFRACTION2chain 'A' and (resid 651 through 739 )
3X-RAY DIFFRACTION3chain 'A' and (resid 740 through 877 )
4X-RAY DIFFRACTION4chain 'A' and (resid 878 through 912 )

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