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- PDB-6eil: DYRK1A in complex with XMD8-49 -

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Basic information

Entry
Database: PDB / ID: 6eil
TitleDYRK1A in complex with XMD8-49
ComponentsDYRK1A
KeywordsTRANSFERASE / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Function / homology
Function and homology information


histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome / amyloid-beta formation / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / non-membrane spanning protein tyrosine kinase activity / tau protein binding / circadian rhythm / peptidyl-tyrosine phosphorylation / : / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein phosphorylation / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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. ...Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-B6B / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.465 Å
AuthorsRothweiler, U.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Novel Scaffolds for Dual Specificity Tyrosine-Phosphorylation-Regulated Kinase (DYRK1A) Inhibitors.
Authors: Czarna, A. / Wang, J. / Zelencova, D. / Liu, Y. / Deng, X. / Choi, H.G. / Zhang, T. / Zhou, W. / Chang, J.W. / Kildalsen, H. / Seternes, O.M. / Gray, N.S. / Engh, R.A. / Rothweiler, U.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 7, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DYRK1A
B: DYRK1A
C: DYRK1A
D: DYRK1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,5807
Polymers170,6164
Non-polymers9643
Water7,746430
1
A: DYRK1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9752
Polymers42,6541
Non-polymers3211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DYRK1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9752
Polymers42,6541
Non-polymers3211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DYRK1A


Theoretical massNumber of molelcules
Total (without water)42,6541
Polymers42,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DYRK1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9752
Polymers42,6541
Non-polymers3211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.390, 87.700, 229.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DYRK1A /


Mass: 42653.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13627
#2: Chemical ChemComp-B6B / [3-azanyl-6-(5-azanyl-2-methoxy-phenyl)pyrazin-2-yl]-pyridin-3-yl-methanone


Mass: 321.333 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H15N5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M KSCN; 0.1M NaCl; 16% PEG 3350, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984003 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984003 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 62269 / % possible obs: 96.1 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rrim(I) all: 0.0044 / Net I/σ(I): 13.76
Reflection shellResolution: 2.46→2.61 Å / Mean I/σ(I) obs: 2.21 / Num. measured obs: 29653 / Num. unique all: 9232 / CC1/2: 0.793 / Rrim(I) all: 0.492

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nct

4nct


Resolution: 2.465→48.16 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.88
RfactorNum. reflection% reflection
Rfree0.2535 3177 5.1 %
Rwork0.2091 --
obs0.2135 62263 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.465→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10940 0 72 430 11442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311278
X-RAY DIFFRACTIONf_angle_d0.56215247
X-RAY DIFFRACTIONf_dihedral_angle_d15.7196735
X-RAY DIFFRACTIONf_chiral_restr0.0411625
X-RAY DIFFRACTIONf_plane_restr0.0031947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4659-2.50840.35611580.29982634X-RAY DIFFRACTION82
2.5084-2.5540.34671340.30752790X-RAY DIFFRACTION89
2.554-2.60310.35251580.29552801X-RAY DIFFRACTION88
2.6031-2.65620.38181450.28542806X-RAY DIFFRACTION88
2.6562-2.71390.31051540.2812778X-RAY DIFFRACTION88
2.7139-2.7770.30561450.28072857X-RAY DIFFRACTION89
2.777-2.84640.34431440.27492892X-RAY DIFFRACTION91
2.8464-2.92330.29391390.2722932X-RAY DIFFRACTION91
2.9233-3.00930.29331570.26282925X-RAY DIFFRACTION91
3.0093-3.10640.31371530.25662999X-RAY DIFFRACTION93
3.1064-3.21730.28081520.23732981X-RAY DIFFRACTION94
3.2173-3.3460.26061550.22683015X-RAY DIFFRACTION94
3.346-3.49810.2671240.21713085X-RAY DIFFRACTION96
3.4981-3.68220.2411670.20733033X-RAY DIFFRACTION94
3.6822-3.91250.23381790.19333009X-RAY DIFFRACTION93
3.9125-4.2140.22982000.16733017X-RAY DIFFRACTION93
4.214-4.63690.20691230.15273115X-RAY DIFFRACTION95
4.6369-5.30520.19791600.16773069X-RAY DIFFRACTION94
5.3052-6.67370.2691460.21153144X-RAY DIFFRACTION95
6.6737-31.73950.23081840.1853264X-RAY DIFFRACTION94

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