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- PDB-7dhk: The co-crystal structure of DYRK2 with a small molecule inhibitor 13 -

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Basic information

Entry
Database: PDB / ID: 7dhk
TitleThe co-crystal structure of DYRK2 with a small molecule inhibitor 13
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 / ubiquitin ligase complex / positive regulation of glycogen biosynthetic process / 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 / ubiquitin ligase complex / positive regulation of glycogen biosynthetic process / 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 / protein phosphorylation / ribonucleoprotein complex / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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-H7O / Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.341 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 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)38,1202
Polymers37,6761
Non-polymers4451
Water1,24369
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 area15770 Å2
Unit cell
Length a, b, c (Å)64.557, 127.838, 132.027
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-H7O / 2-methoxy-7-phenylmethoxy-9-(piperidin-4-ylmethylsulfanyl)acridine


Mass: 444.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.58 Å3/Da / Density % sol: 65.68 %
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: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.341→57.626 Å / Num. obs: 62021 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.971 / Rpim(I) all: 0.12 / Net I/av σ(I): 2.2 / Net I/σ(I): 6
Reflection shellResolution: 2.341→2.43 Å / Rmerge(I) obs: 1.017 / Num. unique obs: 17793 / CC1/2: 0.588 / Rpim(I) all: 0.456

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Processing

Software
NameVersionClassification
PHENIX1.14_3260: ???refinement
XDSdata reduction
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2L

3k2l


Resolution: 2.341→57.626 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 930 5.23 %
Rwork0.1954 16865 -
obs0.1987 17795 75.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.88 Å2 / Biso mean: 42.7477 Å2 / Biso min: 9.3 Å2
Refinement stepCycle: final / Resolution: 2.341→57.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 32 69 2740
Biso mean--46.42 38.42 -
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 (%)
2.341-2.46430.173140.2238260
2.4643-2.61870.3321600.2582109436
2.6187-2.82090.30131550.2632271586
2.8209-3.10480.3431640.23743153100
3.1048-3.5540.26511680.19953174100
3.554-4.47740.21431870.15993156100
Refinement TLS params.Method: refined / Origin x: 76.9309 Å / Origin y: 144.2162 Å / Origin z: 3.6999 Å
111213212223313233
T0.1025 Å20.036 Å2-0.0102 Å2-0.0943 Å20.0055 Å2--0.1196 Å2
L1.276 °20.5224 °20.5077 °2-1.6541 °20.4092 °2--1.8773 °2
S0.0359 Å °0.1193 Å °0.0474 Å °0.0596 Å °0.0669 Å °0.0139 Å °0.0031 Å °0.185 Å °-0.0435 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA215 - 538
2X-RAY DIFFRACTION1allS1 - 72
3X-RAY DIFFRACTION1allB1

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