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- PDB-7dh3: The co-crystal structure of DYRK2 with a small molecule inhibitor 5 -

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Basic information

Entry
Database: PDB / ID: 7dh3
TitleThe co-crystal structure of DYRK2 with a small molecule inhibitor 5
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
2,7-dimethoxy-9-piperidin-4-ylsulfanyl-acridine / Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsWei, T. / Xiao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: The co-crystal structure of DYRK2 with a small molecule inhibitor 5
Authors: Wei, T. / Xiao, J.
History
DepositionNov 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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)38,2262
Polymers37,8721
Non-polymers3541
Water1,15364
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 area16130 Å2
Unit cell
Length a, b, c (Å)64.560, 128.830, 132.450
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: 37871.875 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-H7C / 2,7-dimethoxy-9-piperidin-4-ylsulfanyl-acridine


Mass: 354.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.62 Å3/Da / Density % sol: 66.06 %
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: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→66.22 Å / Num. obs: 23161 / % possible obs: 96.4 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Net I/σ(I): 15.9
Reflection shellResolution: 2.33→2.39 Å / Rmerge(I) obs: 1.102 / Num. unique obs: 1751 / CC1/2: 0.807 / Rpim(I) all: 0.311

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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: 2.33→36.417 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 1127 4.87 %
Rwork0.1938 22000 -
obs0.195 23127 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.62 Å2 / Biso mean: 56.1622 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.33→36.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 25 64 2742
Biso mean--52.01 52.12 -
Num. residues----326
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.33-2.4360.31061430.24872770100
2.436-2.56440.29871550.24492817100
2.5644-2.72510.26851590.23742795100
2.7251-2.93540.24961460.23232831100
2.9354-3.23060.25581500.21532834100
3.2306-3.69770.2347940.2054227679
3.6977-4.65720.16661270.1624268193

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