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- PDB-7z5w: ROS1 with AstraZeneca ligand 1 -

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Basic information

Entry
Database: PDB / ID: 7z5w
TitleROS1 with AstraZeneca ligand 1
ComponentsProto-oncogene tyrosine-protein kinase ROS
KeywordsTRANSFERASE / Virtual Screening / Potent Selective / ROS1 / Kinase Inhibitors
Function / homology
Function and homology information


columnar/cuboidal epithelial cell development / regulation of TOR signaling / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / regulation of ERK1 and ERK2 cascade / regulation of cell growth / receptor protein-tyrosine kinase / spermatogenesis / protein phosphatase binding / protein tyrosine kinase activity ...columnar/cuboidal epithelial cell development / regulation of TOR signaling / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / regulation of ERK1 and ERK2 cascade / regulation of cell growth / receptor protein-tyrosine kinase / spermatogenesis / protein phosphatase binding / protein tyrosine kinase activity / cell differentiation / receptor complex / protein phosphorylation / ATP binding / membrane / plasma membrane
Similarity search - Function
LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Six-bladed beta-propeller, TolB-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Six-bladed beta-propeller, TolB-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III 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, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-IDW / Proto-oncogene tyrosine-protein kinase ROS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.254 Å
AuthorsHargreaves, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Chem.Inf.Model. / Year: 2022
Title: Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors.
Authors: Petrovic, D. / Scott, J.S. / Bodnarchuk, M.S. / Lorthioir, O. / Boyd, S. / Hughes, G.M. / Lane, J. / Wu, A. / Hargreaves, D. / Robinson, J. / Sadowski, J.
History
DepositionMar 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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: Proto-oncogene tyrosine-protein kinase ROS
B: Proto-oncogene tyrosine-protein kinase ROS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3356
Polymers75,3022
Non-polymers1,0334
Water1,946108
1
A: Proto-oncogene tyrosine-protein kinase ROS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1683
Polymers37,6511
Non-polymers5172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene tyrosine-protein kinase ROS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1683
Polymers37,6511
Non-polymers5172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.700, 41.340, 85.540
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase ROS / Proto-oncogene c-Ros / Proto-oncogene c-Ros-1 / Receptor tyrosine kinase c-ros oncogene 1 / c-Ros ...Proto-oncogene c-Ros / Proto-oncogene c-Ros-1 / Receptor tyrosine kinase c-ros oncogene 1 / c-Ros receptor tyrosine kinase


Mass: 37650.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROS1, MCF3, ROS / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P08922, receptor protein-tyrosine kinase
#2: Chemical ChemComp-IDW / ~{N}-[6-methyl-2-[(2~{S})-2-[3-(3-methylpyrazin-2-yl)-1,2-oxazol-5-yl]pyrrolidin-1-yl]pyrimidin-4-yl]-1,3-thiazol-2-amine


Mass: 420.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N8OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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

CrystalDescription: plate like
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.66
Details: 11% peg3350, 200mM AmSO4, PCTP 100mM pH 6.66. Grown in 15well plate. Seeded with previous crystals. ATP/Mg 10mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→42.77 Å / Num. obs: 25992 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 1 / Rmerge(I) obs: 0.089 / Net I/σ(I): 0.998
Reflection shellResolution: 2.25→2.31 Å / Rmerge(I) obs: 1.339 / Num. unique obs: 1817

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (24-FEB-2021)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UXL

4uxl


Resolution: 2.254→42.77 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.373 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.259
RfactorNum. reflection% reflectionSelection details
Rfree0.2755 1300 5 %RANDOM
Rwork0.2232 ---
obs0.2258 25983 99.4 %-
Displacement parametersBiso max: 99.79 Å2 / Biso mean: 62.52 Å2 / Biso min: 39.28 Å2
Baniso -1Baniso -2Baniso -3
1--3.8132 Å20 Å22.6803 Å2
2--1.6156 Å20 Å2
3---2.1975 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.254→42.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 70 108 4520
Biso mean--57.3 61.4 -
Num. residues----543
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1563SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes747HARMONIC5
X-RAY DIFFRACTIONt_it4520HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion564SEMIHARMONIC5
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_contact3688SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4520HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6135HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion20.35
LS refinement shellResolution: 2.254→2.27 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3454 26 5 %
Rwork0.3214 494 -
obs--80.03 %

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