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- PDB-6eiv: DYRK1A in complex with JWD-065 -

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Basic information

Entry
Database: PDB / ID: 6eiv
TitleDYRK1A in complex with JWD-065
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 1A
KeywordsTRANSFERASE / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Function / homology
Function and homology information


regulation of amyloid-beta formation / negative regulation of heterochromatin formation / regulation of neurofibrillary tangle assembly / histone H3T45 kinase activity / dual-specificity kinase / splicing factor binding / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / regulation of alternative mRNA splicing, via spliceosome / negative regulation of microtubule polymerization ...regulation of amyloid-beta formation / negative regulation of heterochromatin formation / regulation of neurofibrillary tangle assembly / histone H3T45 kinase activity / dual-specificity kinase / splicing factor binding / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / regulation of alternative mRNA splicing, via spliceosome / negative regulation of microtubule polymerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / RNA polymerase II CTD heptapeptide repeat kinase activity / tubulin binding / peptidyl-tyrosine phosphorylation / positive regulation of RNA splicing / non-membrane spanning protein tyrosine kinase activity / circadian rhythm / tau protein binding / nervous system development / actin binding / protein autophosphorylation / protein tyrosine kinase activity / transcription coactivator activity / protein phosphorylation / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / centrosome / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
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. ...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-B6Q / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.68 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 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,4748
Polymers170,6164
Non-polymers1,8584
Water2,234124
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1192
Polymers42,6541
Non-polymers4651
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)43,1192
Polymers42,6541
Non-polymers4651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1192
Polymers42,6541
Non-polymers4651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1192
Polymers42,6541
Non-polymers4651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.760, 88.540, 231.120
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
Dual specificity tyrosine-phosphorylation-regulated kinase 1A / Dual specificity YAK1-related kinase / HP86 / Protein kinase minibrain homolog / hMNB


Mass: 42653.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Production host: Escherichia coli (E. coli) / References: UniProt: Q13627, dual-specificity kinase
#2: Chemical
ChemComp-B6Q / ~{N}-[3-[[4-azanyl-2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]-1,3-thiazol-5-yl]carbonyl]phenyl]propanamide


Mass: 464.583 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H28N6O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M KSCN; 0.05M LiCl; 10% PEG 3350, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 51533 / % possible obs: 99 % / Redundancy: 5.7 % / Rrim(I) all: 0.146 / Net I/σ(I): 9.74
Reflection shellResolution: 2.68→2.84 Å / Mean I/σ(I) obs: 1.7 / Num. measured obs: 40704 / Num. unique all: 7897 / Rrim(I) all: 0.768

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.68→48.623 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.46
RfactorNum. reflection% reflection
Rfree0.2355 2651 5.15 %
Rwork0.1965 --
obs0.1998 51524 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.68→48.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10911 0 132 124 11167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311313
X-RAY DIFFRACTIONf_angle_d0.71915296
X-RAY DIFFRACTIONf_dihedral_angle_d13.7834291
X-RAY DIFFRACTIONf_chiral_restr0.0251622
X-RAY DIFFRACTIONf_plane_restr0.0031956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6833-2.73210.3351410.29982346X-RAY DIFFRACTION88
2.7321-2.78460.33021090.30032594X-RAY DIFFRACTION96
2.7846-2.84140.34681420.29122535X-RAY DIFFRACTION95
2.8414-2.90320.36181300.28492530X-RAY DIFFRACTION95
2.9032-2.97070.27791440.26272549X-RAY DIFFRACTION94
2.9707-3.04490.28781170.26722594X-RAY DIFFRACTION96
3.0449-3.12720.32021330.2472537X-RAY DIFFRACTION95
3.1272-3.21910.26331450.24472539X-RAY DIFFRACTION94
3.2191-3.32290.29041520.22642531X-RAY DIFFRACTION94
3.3229-3.44160.2551570.2192557X-RAY DIFFRACTION94
3.4416-3.57920.26581410.20622561X-RAY DIFFRACTION94
3.5792-3.74190.22651270.19992576X-RAY DIFFRACTION95
3.7419-3.93890.21491280.18162577X-RAY DIFFRACTION95
3.9389-4.18520.18461440.17032593X-RAY DIFFRACTION94
4.1852-4.50760.20671470.15332573X-RAY DIFFRACTION94
4.5076-4.95980.22271440.15012603X-RAY DIFFRACTION94
4.9598-5.67430.19691440.17352618X-RAY DIFFRACTION95
5.6743-7.13690.24321530.18962636X-RAY DIFFRACTION94
7.1369-32.82120.19151410.17272795X-RAY DIFFRACTION95

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