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- PDB-5sav: DDR1, N-[2-[3-(2-aminopyrimidin-5-yl)oxyphenyl]ethyl]-3-(trifluor... -

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Basic information

Entry
Database: PDB / ID: 5sav
TitleDDR1, N-[2-[3-(2-aminopyrimidin-5-yl)oxyphenyl]ethyl]-3-(trifluoromethoxy)benzamide, 1.760A, P212121, Rfree=23.5%
ComponentsEpithelial discoidin domain-containing receptor 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / RTK / RECEPTOR TYROSINE KINASE / COLLAGEN / DISCOIDIN DOMAIN / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-1IJ / IODIDE ION / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsStihle, M. / Richter, H. / Benz, J. / Hochstrasser, R. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche Switzerland
CitationJournal: To be published
Title: Crystal Structure of a DDR1 complex
Authors: Richter, H. / Prunotto, M. / Kuhn, B. / Rudolph, M.G.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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)37,3025
Polymers36,5031
Non-polymers7994
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.000, 62.560, 109.280
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: Deletion of residues 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-1IJ / N-(2-{3-[(2-aminopyrimidin-5-yl)oxy]phenyl}ethyl)-3-(trifluoromethoxy)benzamide


Mass: 418.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17F3N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 7.6 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed with reservoir consisting of 0.1M MES/NaOH pH 6.5, 0.2M KI, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→41.15 Å / Num. obs: 30720 / % possible obs: 99.9 % / Redundancy: 6.55 % / Biso Wilson estimate: 22.05 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.208 / Rrim(I) all: 0.23 / Rsym value: 0.208 / Χ2: 0.914 / Net I/σ(I): 6.74 / Num. measured all: 199573
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.76-1.816.742.0280.8914976222322220.2882.198100
1.81-1.866.6171.823114332216621660.3461.98100
1.86-1.916.3581.5441.2313607214121400.3411.683100
1.91-1.976.3341.261.5613004205320530.4511.374100
1.97-2.036.7131.0432.0613399199619960.6231.132100
2.03-2.16.6370.8722.5612882194419410.7110.94799.8
2.1-2.186.4890.713.1712140187418710.8190.77399.8
2.18-2.276.2930.583.7511108176817650.8620.63399.8
2.27-2.376.090.4524.7610670175317520.9030.49499.9
2.37-2.496.680.3645.9511115166516640.9470.39599.9
2.49-2.626.7330.2927.2910719159215920.9660.316100
2.62-2.786.7250.2278.9110094150115010.9790.246100
2.78-2.976.2860.17710.418964142614260.9840.193100
2.97-3.216.5610.1413.038634131613160.990.152100
3.21-3.526.8380.10117.218452123612360.9940.109100
3.52-3.946.610.07920.047443112611260.9960.086100
3.94-4.546.0460.06322.4560049939930.9960.069100
4.54-5.576.4830.06522.6955828618610.9970.071100
5.57-7.876.0980.06421.7641716846840.9960.071100
7.87-41.1535.5270.04227.7822774184120.9980.04698.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1539refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.76→41.153 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.44 / Stereochemistry target values: ML
Details: torsion angle in ether is outside preferred region. one fluorine clashes with protein
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 1548 5.05 %RANDOM
Rwork0.1925 29100 --
obs0.1947 30648 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.84 Å2 / Biso mean: 29.2725 Å2 / Biso min: 8.76 Å2
Refinement stepCycle: final / Resolution: 1.76→41.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 33 264 2630
Biso mean--23.4 34.42 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072460
X-RAY DIFFRACTIONf_angle_d1.1183337
X-RAY DIFFRACTIONf_chiral_restr0.042355
X-RAY DIFFRACTIONf_plane_restr0.005438
X-RAY DIFFRACTIONf_dihedral_angle_d13.639955
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7601-1.81690.38361310.320125822713
1.8169-1.88180.31711360.309226092745
1.8818-1.95710.2951400.282626132753
1.9571-2.04620.30481300.247826022732
2.0462-2.15410.26441520.222626042756
2.1541-2.2890.28091390.209426292768
2.289-2.46580.22821420.193126472789
2.4658-2.71390.26931390.18126322771
2.7139-3.10640.22031460.18226542800
3.1064-3.91330.20251680.155126772845
3.9133-41.16460.17871250.161828512976
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)
12.61070.1722-0.88672.7421-0.06562.08220.44470.69850.3963-0.2523-0.3976-0.0512-0.275-0.27530.01560.40230.10110.07660.45360.04720.3492-16.4309-4.1128-2.0787
21.1001-0.7372-0.32962.09690.57221.15740.21920.2270.0983-0.3051-0.2896-0.0318-0.1118-0.1740.02850.24720.01330.02290.2153-0.00170.1498-17.5426-1.11416.9173
31.4986-1.63291.77364.0511-1.10693.27960.12810.3847-0.1132-0.4288-0.2749-0.47220.42120.39480.07430.2388-0.00850.070.2281-0.02810.2537-7.9079-27.152114.9698
41.15150.4263-0.25111.6286-0.6691.0870.006-0.0331-0.00750.09880.00350.0275-0.006-0.0171-0.00610.11310.00680.00140.1022-0.01160.1006-14.8326-12.970229.2697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 602 through 636 )A602 - 636
2X-RAY DIFFRACTION2chain 'A' and (resid 648 through 708 )A648 - 708
3X-RAY DIFFRACTION3chain 'A' and (resid 709 through 733 )A709 - 733
4X-RAY DIFFRACTION4chain 'A' and (resid 734 through 903 )A734 - 903

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