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- PDB-6k0j: The co-crystal structure of DYRK2 with a small molecule inhibitor -

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Basic information

Entry
Database: PDB / ID: 6k0j
TitleThe co-crystal structure of DYRK2 with a small molecule inhibitor
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 2
KeywordsTRANSFERASE/INHIBITOR / kinase / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of glycogen biosynthetic process / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity ...dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of glycogen biosynthetic process / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity / Regulation of TP53 Activity through Phosphorylation / cytoskeleton / ribonucleoprotein complex / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Dual specificity tyrosine-phosphorylation-regulated kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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-CQO / Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.352 Å
AuthorsTiantian, W. / Xiao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression.
Authors: Banerjee, S. / Wei, T. / Wang, J. / Lee, J.J. / Gutierrez, H.L. / Chapman, O. / Wiley, S.E. / Mayfield, J.E. / Tandon, V. / Juarez, E.F. / Chavez, L. / Liang, R. / Sah, R.L. / Costello, C. / ...Authors: Banerjee, S. / Wei, T. / Wang, J. / Lee, J.J. / Gutierrez, H.L. / Chapman, O. / Wiley, S.E. / Mayfield, J.E. / Tandon, V. / Juarez, E.F. / Chavez, L. / Liang, R. / Sah, R.L. / Costello, C. / Mesirov, J.P. / de la Vega, L. / Cooper, K.L. / Dixon, J.E. / Xiao, J. / Lei, X.
History
DepositionMay 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity tyrosine-phosphorylation-regulated kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0992
Polymers37,7711
Non-polymers3281
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15930 Å2
Unit cell
Length a, b, c (Å)64.487, 129.127, 132.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-872-

HOH

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Components

#1: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 2


Mass: 37770.676 Da / Num. of mol.: 1 / Fragment: UNP residues 212-536 / Mutation: E256N, L349A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q92630, dual-specificity kinase
#2: Chemical ChemComp-CQO / 3-(2,7-dimethoxyacridin-9-yl)sulfanylpropan-1-amine


Mass: 328.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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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: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.36 M-0.5 M sodium citrate tribasic dihydrate, 0.01 M sodium borate, pH 7.5-9.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.352→50 Å / Num. obs: 23261 / % possible obs: 99.13 % / Redundancy: 13.2 % / Net I/σ(I): 24.6
Reflection shellResolution: 2.352→2.44 Å / Num. unique obs: 2167

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.352→46.305 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.03
RfactorNum. reflection% reflection
Rfree0.2093 2000 8.6 %
Rwork0.172 --
obs0.1751 23261 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.352→46.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2646 0 23 181 2850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082735
X-RAY DIFFRACTIONf_angle_d0.9663688
X-RAY DIFFRACTIONf_dihedral_angle_d10.9171645
X-RAY DIFFRACTIONf_chiral_restr0.054388
X-RAY DIFFRACTIONf_plane_restr0.007470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3524-2.41130.28791310.21011399X-RAY DIFFRACTION92
2.4113-2.47650.23581400.20741485X-RAY DIFFRACTION98
2.4765-2.54930.23071390.20211471X-RAY DIFFRACTION99
2.5493-2.63160.25711400.20391493X-RAY DIFFRACTION100
2.6316-2.72560.25461430.19361519X-RAY DIFFRACTION100
2.7256-2.83480.2361420.1921511X-RAY DIFFRACTION100
2.8348-2.96380.24691430.18681523X-RAY DIFFRACTION100
2.9638-3.120.241440.18861518X-RAY DIFFRACTION100
3.12-3.31540.26571430.18781530X-RAY DIFFRACTION100
3.3154-3.57130.22811440.17181525X-RAY DIFFRACTION100
3.5713-3.93050.18281440.14871531X-RAY DIFFRACTION100
3.9305-4.49890.14031450.14191550X-RAY DIFFRACTION100
4.4989-5.66650.20131480.14941560X-RAY DIFFRACTION100
5.6665-46.3140.16861540.1711646X-RAY DIFFRACTION100

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