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- PDB-5fdx: Structure of DDR1 receptor tyrosine kinase in complex with D2164 ... -

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Basic information

Entry
Database: PDB / ID: 5fdx
TitleStructure of DDR1 receptor tyrosine kinase in complex with D2164 inhibitor at 2.65 Angstroms resolution.
ComponentsEpithelial discoidin domain-containing receptor 1
KeywordsTRANSFERASE / DDR1 Kinase / inhibitors / Structural Genomics / PSI-Biology / 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 / collagen binding / lactation / embryo implantation / transmembrane receptor protein tyrosine kinase activity / regulation of cell growth / cell surface receptor protein tyrosine kinase signaling pathway / receptor protein-tyrosine kinase / positive regulation of neuron projection development / 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 / 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-5X1 / DI(HYDROXYETHYL)ETHER / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBartual, S.G. / Pinkas, D.M. / Wang, Z. / Ding, K. / Mahajan, P. / Kupinska, K. / Mukhopadhyay, S. / Strain-Damerell, C. / Chalk, R. / Borkowska, O. ...Bartual, S.G. / Pinkas, D.M. / Wang, Z. / Ding, K. / Mahajan, P. / Kupinska, K. / Mukhopadhyay, S. / Strain-Damerell, C. / Chalk, R. / Borkowska, O. / Talon, R. / Kopec, J. / Williams, E. / Tallant, C. / Chaikuad, A. / Sorell, F. / Newman, J. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Structure of DDR1 receptor tyrosine kinase in complex with D2164 inhibitor at 2.65 Angstroms resolution.
Authors: Bartual, S.G. / Ding, K. / Wang, Z. / Bullock, N.A.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Jan 10, 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
B: Epithelial discoidin domain-containing receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,24312
Polymers76,5662
Non-polymers1,67810
Water2,540141
1
A: Epithelial discoidin domain-containing receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1627
Polymers38,2831
Non-polymers8796
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)39,0825
Polymers38,2831
Non-polymers7994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.548, 120.340, 63.020
Angle α, β, γ (deg.)90.00, 94.87, 90.00
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 / DDR1 receptor tyrosine kinase


Mass: 38282.805 Da / Num. of mol.: 2 / Fragment: UNP Residues 601-913
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-5X1 / 3-[(4-methylpiperazin-1-yl)methyl]-~{N}-[(4~{R})-4-methyl-2-pyrimidin-5-yl-3,4-dihydro-1~{H}-isoquinolin-7-yl]-5-(trifluoromethyl)benzamide


Mass: 524.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31F3N6O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350 10% ethylene glycol 0.1M bis-tris-propane pH6.5 0.2M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92818 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92818 Å / Relative weight: 1
ReflectionResolution: 2.65→43.44 Å / Num. obs: 19393 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 54.08 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.072 / Net I/σ(I): 5.5
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 0.8 / Rpim(I) all: 0.629 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CKR

4ckr


Resolution: 2.65→43.44 Å / Cor.coef. Fo:Fc: 0.9196 / Cor.coef. Fo:Fc free: 0.8647 / SU R Cruickshank DPI: 1.058 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.921 / SU Rfree Blow DPI: 0.344 / SU Rfree Cruickshank DPI: 0.352
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 961 4.96 %RANDOM
Rwork0.194 ---
obs0.198 19357 98.37 %-
Displacement parametersBiso mean: 58.82 Å2
Baniso -1Baniso -2Baniso -3
1--11.976 Å20 Å26.9601 Å2
2---1.7601 Å20 Å2
3---13.7361 Å2
Refine analyzeLuzzati coordinate error obs: 0.381 Å
Refinement stepCycle: LAST / Resolution: 2.65→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 117 141 4569
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014529HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.096127HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1541SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes655HARMONIC5
X-RAY DIFFRACTIONt_it4529HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion19.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion565SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5034SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.79 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2796 141 5.01 %
Rwork0.2365 2675 -
all0.2386 2816 -
obs--98.91 %
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)
10.55960.1283-0.08422.3013-0.60782.0141-0.0869-0.02030.05920.01360.07210.0642-0.2374-0.28510.01480.12740.05340.0377-0.1625-0.0187-0.22591.7435-25.4277-23.7654
20.70920.20350.96221.86560.29683.50050.0816-0.1496-0.12530.0180.0337-0.14230.5275-0.0217-0.11540.15050.00260.0886-0.210.0297-0.280511.1351-40.50568.9469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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