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- PDB-7dhc: The co-crystal structure of DYRK2 with a small molecule inhibitor 10 -

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Basic information

Entry
Database: PDB / ID: 7dhc
TitleThe co-crystal structure of DYRK2 with a small molecule inhibitor 10
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-H99 / Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.592 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 13, 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 1.3Nov 13, 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)38,0942
Polymers37,6761
Non-polymers4191
Water84747
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 area15740 Å2
Unit cell
Length a, b, c (Å)64.427, 128.382, 132.446
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-H99 / 4-[bis(fluoranyl)methyl]-2,7-dimethoxy-9-(piperidin-4-ylmethylsulfanyl)acridine


Mass: 418.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24F2N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.63 Å3/Da / Density % sol: 66.16 %
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: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 25487 / % possible obs: 99.4 % / Redundancy: 5.4 % / CC1/2: 0.956 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.066 / Net I/σ(I): 11.6
Reflection shellResolution: 2.59→2.69 Å / Rmerge(I) obs: 0.138 / Num. unique obs: 1219 / CC1/2: 0.786 / Rpim(I) all: 0.448

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Processing

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

3k2l


Resolution: 2.592→46.092 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 2525 9.91 %
Rwork0.1642 22962 -
obs0.1697 25487 77.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.78 Å2 / Biso mean: 42.3104 Å2 / Biso min: 9.15 Å2
Refinement stepCycle: final / Resolution: 2.592→46.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 29 47 2715
Biso mean--43.56 36.8 -
Num. residues----324
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5921-2.64190.396600.362754033
2.6419-2.69590.379810.294573745
2.6959-2.75450.2908960.256187752
2.7545-2.81850.2586950.229988755
2.8185-2.8890.29781080.216197958
2.889-2.96710.27351130.2222101362
2.9671-3.05440.26551280.1974115170
3.0544-3.1530.2291430.1992124375
3.153-3.26560.241420.2035137582
3.2656-3.39630.23241570.1837145889
3.3963-3.55090.23411780.1619158297
3.5509-3.7380.24411770.1517164399
3.738-3.97210.2031840.14121648100
3.9721-4.27860.20081850.13891649100
4.2786-4.70870.14861790.124162799
4.7087-5.38920.2261800.1436161598
5.3892-6.78640.22381580.1741150591
Refinement TLS params.Method: refined / Origin x: 76.7024 Å / Origin y: 144.8661 Å / Origin z: 3.8137 Å
111213212223313233
T0.0974 Å20.0226 Å2-0.007 Å2-0.1093 Å20.0145 Å2--0.111 Å2
L1.0405 °20.4441 °20.5808 °2-1.4317 °20.4027 °2--1.3993 °2
S0.0339 Å °0.0957 Å °0.0854 Å °0.04 Å °0.0803 Å °0.0463 Å °0.0005 Å °0.1383 Å °0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA215 - 539
2X-RAY DIFFRACTION1allS1 - 51

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