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- PDB-7aka: Structure of DYRK1A in complex with compound 54 -

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Basic information

Entry
Database: PDB / ID: 7aka
TitleStructure of DYRK1A in complex with compound 54
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 1A
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / PHOSPHOPROTEIN / KINASE SELECTIVITY / SBDD / SMALL MOLECULE INHIBITOR
Function / homology
Function and homology information


negative regulation of heterochromatin formation / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / negative regulation of microtubule polymerization / amyloid-beta formation / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome ...negative regulation of heterochromatin formation / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / negative regulation of microtubule polymerization / amyloid-beta formation / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / RNA polymerase II CTD heptapeptide repeat kinase activity / protein serine/threonine/tyrosine kinase activity / tubulin binding / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / tau protein binding / circadian rhythm / actin binding / nervous system development / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / transcription coactivator activity / histone H3T45 kinase activity / cytoskeleton / protein kinase activity / nuclear speck / protein phosphorylation / ribonucleoprotein complex / axon / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / : / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / : / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
PHOSPHATE ION / Chem-RK2 / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsDokurno, P. / Surgenor, A.E. / Kotschy, A.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Guided Discovery of Potent and Selective DYRK1A Inhibitors.
Authors: Weber, C. / Sipos, M. / Paczal, A. / Balint, B. / Kun, V. / Foloppe, N. / Dokurno, P. / Massey, A.J. / Walmsley, D.L. / Hubbard, R.E. / Murray, J. / Benwell, K. / Edmonds, T. / Demarles, D. ...Authors: Weber, C. / Sipos, M. / Paczal, A. / Balint, B. / Kun, V. / Foloppe, N. / Dokurno, P. / Massey, A.J. / Walmsley, D.L. / Hubbard, R.E. / Murray, J. / Benwell, K. / Edmonds, T. / Demarles, D. / Bruno, A. / Burbridge, M. / Cruzalegui, F. / Kotschy, A.
History
DepositionSep 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 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 1A
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2547
Polymers83,2942
Non-polymers9595
Water5,729318
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1013
Polymers41,6471
Non-polymers4542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1534
Polymers41,6471
Non-polymers5063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.827, 84.616, 84.239
Angle α, β, γ (deg.)90.000, 107.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 1A / Dual specificity YAK1-related kinase / HP86 / Protein kinase minibrain homolog / hMNB


Mass: 41647.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Cell line (production host): pLysS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13627, dual-specificity kinase

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Non-polymers , 5 types, 323 molecules

#2: Chemical ChemComp-RK2 / 4-[2-methyl-3-[(2~{R})-2-pyridin-2-yloxypropyl]imidazo[4,5-b]pyridin-5-yl]pyridine-2,6-diamine


Mass: 375.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG4k, 0.2M Mg chloride, 0.1M MES buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.77→29.1 Å / Num. obs: 70661 / % possible obs: 93.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.4
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 1.6 % / Rmerge(I) obs: 2.05 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1 / % possible all: 56.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vx3

2vx3


Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.588 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 2902 4.9 %RANDOM
Rwork0.1724 ---
obs0.1742 56689 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.58 Å2 / Biso mean: 36.798 Å2 / Biso min: 20.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å20 Å2-1.67 Å2
2---1.61 Å20 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5416 0 66 318 5800
Biso mean--41.35 41.11 -
Num. residues----669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135628
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175279
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6457605
X-RAY DIFFRACTIONr_angle_other_deg1.3161.57512218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47321.736288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09715999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6851537
X-RAY DIFFRACTIONr_chiral_restr0.0790.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021217
LS refinement shellResolution: 1.9→2.002 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.335 446 -
Rwork0.306 8160 -
all-8606 -
obs--97.37 %

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