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- PDB-7djo: The co-crystal structure of DYRK2 with a small molecule inhibitor 17 -

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Basic information

Entry
Database: PDB / ID: 7djo
TitleThe co-crystal structure of DYRK2 with a small molecule inhibitor 17
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 2
KeywordsCELL CYCLE / kinase / inhibitor
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 / 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
Similarity search - Domain/homology
Chem-H80 / Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsWei, T. / Xiao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Elife / Year: 2022
Title: Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry.
Authors: Wei, T. / Wang, J. / Liang, R. / Chen, W. / Chen, Y. / Ma, M. / He, A. / Du, Y. / Zhou, W. / Zhang, Z. / Zeng, X. / Wang, C. / Lu, J. / Guo, X. / Chen, X.W. / Wang, Y. / Tian, R. / Xiao, J. / Lei, X.
History
DepositionNov 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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: Dual specificity tyrosine-phosphorylation-regulated kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0602
Polymers37,6761
Non-polymers3841
Water1,946108
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 area15900 Å2
Unit cell
Length a, b, c (Å)64.955, 128.929, 133.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 37675.633 Da / Num. of mol.: 1
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-H80 / [2,7-dimethoxy-9-[[(3S)-pyrrolidin-3-yl]methylsulfanyl]acridin-4-yl]methanol


Mass: 384.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / 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

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.36 M-0.5 M sodium citrate tribasic dehydrate, 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: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.492→50 Å / Num. obs: 27095 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.996 / Rpim(I) all: 0.038 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 1083 / CC1/2: 0.81 / Rpim(I) all: 0.225

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2L

3k2l


Resolution: 2.499→46.378 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1829 10 %
Rwork0.1779 16458 -
obs0.1836 18287 92.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.5 Å2 / Biso mean: 40.8046 Å2 / Biso min: 11.4 Å2
Refinement stepCycle: final / Resolution: 2.499→46.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 27 108 2774
Biso mean--41.79 42.5 -
Num. residues----322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.56630.3248780.246970052
2.5663-2.64180.3221060.228495271
2.6418-2.72710.34111310.2172118587
2.7271-2.82450.27311470.2059132297
2.8245-2.93760.271480.2102133299
2.9376-3.07120.29641520.21891361100
3.0712-3.23310.30011520.21321375100
3.2331-3.43560.22731530.19191376100
3.4356-3.70080.22131500.16551342100
3.7008-4.0730.2261530.15511380100
4.073-4.66190.18041530.13751385100
4.6619-5.87170.22341530.1564136898
Refinement TLS params.Method: refined / Origin x: 77.6387 Å / Origin y: 145.3943 Å / Origin z: 3.7584 Å
111213212223313233
T0.1333 Å20.0111 Å2-0.0329 Å2-0.1461 Å2-0.0046 Å2--0.1421 Å2
L0.4708 °20.3272 °20.2125 °2-0.8437 °20.2971 °2--0.6584 °2
S0.0545 Å °0.0397 Å °0.006 Å °0.0657 Å °0.0653 Å °-0.0161 Å °0.0154 Å °0.0957 Å °0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA215 - 538
2X-RAY DIFFRACTION1allS1 - 116
3X-RAY DIFFRACTION1allS117
4X-RAY DIFFRACTION1allB1

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