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- PDB-8c2z: Crystal structure of DYRK1B in complex with AZ191 -

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Basic information

Entry
Database: PDB / ID: 8c2z
TitleCrystal structure of DYRK1B in complex with AZ191
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 1B
KeywordsTRANSFERASE / Kinase / diabetes / kinase inhibitor
Function / homology
Function and homology information


myoblast fusion / dual-specificity kinase / adipose tissue development / protein serine/threonine/tyrosine kinase activity / chromosome / protein tyrosine kinase activity / transcription coactivator activity / protein kinase activity / protein phosphorylation / protein serine kinase activity ...myoblast fusion / dual-specificity kinase / adipose tissue development / protein serine/threonine/tyrosine kinase activity / chromosome / protein tyrosine kinase activity / transcription coactivator activity / protein kinase activity / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / 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-QS0 / Dual specificity tyrosine-phosphorylation-regulated kinase 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsGrygier, P. / Pustelny, K. / Dubin, G. / Czarna, A.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2019/34/E/NZ1/00467 Poland
National Center for Research and Development (Poland)PPN/PPO/2018/1/00046 Poland
CitationJournal: To Be Published
Title: Structural perspective on the design of selective DYRK1B inhibitors
Authors: Grygier, P. / Pustelny, K. / Dubin, G. / Czarna, A.
History
DepositionDec 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,4985
Polymers42,9041
Non-polymers5944
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-12 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.896, 121.509, 54.021
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

#1: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 1B / Minibrain-related kinase / Mirk protein kinase


Mass: 42904.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1B, MIRK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y463, dual-specificity kinase
#2: Chemical ChemComp-QS0 / N-[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]-4-(1-methylpyrrolo[2,3-c]pyridin-3-yl)pyrimidin-2-amine / N-[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]-4-(1-methylpyrrolo[2,3-c]pyridin-3-yl)pyrimidin-2-amine


Mass: 429.517 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C24H27N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.5, 25% PEG3350, 0.2 M magnesium chloride, 0.1 M manganese (II) chloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.91→45.41 Å / Num. obs: 29064 / % possible obs: 97.1 % / Redundancy: 8.3 % / Biso Wilson estimate: 38.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.029 / Rrim(I) all: 0.083 / Χ2: 1.04 / Net I/σ(I): 13.8 / Num. measured all: 242154
Reflection shellResolution: 1.91→1.95 Å / % possible obs: 97.8 % / Redundancy: 8.5 % / Rmerge(I) obs: 2.035 / Num. measured all: 16608 / Num. unique obs: 1945 / CC1/2: 0.453 / Rpim(I) all: 0.726 / Rrim(I) all: 2.164 / Χ2: 1.08 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→45.41 Å / SU ML: 0.2807 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7947
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 1488 5.12 %
Rwork0.1767 27567 -
obs0.1789 29055 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.03 Å2
Refinement stepCycle: LAST / Resolution: 1.91→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 35 185 2879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332760
X-RAY DIFFRACTIONf_angle_d1.31533739
X-RAY DIFFRACTIONf_chiral_restr0.0792405
X-RAY DIFFRACTIONf_plane_restr0.0129492
X-RAY DIFFRACTIONf_dihedral_angle_d15.65341043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.970.38211290.34322456X-RAY DIFFRACTION97.07
1.97-2.040.32171440.28262493X-RAY DIFFRACTION97.23
2.04-2.120.2771200.22842476X-RAY DIFFRACTION96.58
2.12-2.220.25851250.21142366X-RAY DIFFRACTION92.16
2.22-2.340.23041480.19212502X-RAY DIFFRACTION97.53
2.34-2.480.26871490.19542502X-RAY DIFFRACTION98.26
2.48-2.680.2421390.18512522X-RAY DIFFRACTION98.41
2.68-2.950.23591210.18052558X-RAY DIFFRACTION97.95
2.95-3.370.21871280.17812462X-RAY DIFFRACTION94.22
3.37-4.250.19111390.14842600X-RAY DIFFRACTION98.99
4.25-45.410.19161460.15972630X-RAY DIFFRACTION95.89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.59103312069-0.824844561071-1.606946687345.979480602940.5279237494517.725008587140.2397599305530.218726606814-0.274821372127-0.620151400834-0.156718574318-0.3772478569290.8359691545070.0907377116992-0.148946269730.3994595912520.06169429933360.006661969678010.3575810588930.1035093412880.463312032178-9.22193855471-34.25418642144.84453868738
21.04837783773-0.3448260746531.193538393182.8571312573-0.860998430751.542457846420.0281402929310.056466879085-0.000462138198757-0.0388237312458-0.241618608229-0.3904301034860.1430776287840.2492993197060.2272799631770.2522755866060.02731786836690.07988563504150.3344007599350.07474315523910.31182708708-16.0660030233-17.2817082247-0.993329403315
31.63081695185-0.33082226763-0.4476219387971.351709929920.03390757069734.559135172280.04649788877320.2041191637130.03587343481-0.438695232352-0.212768330989-0.01023763588480.1201541665590.1347462770310.1696709543460.3557800389790.05066592768030.01893553434470.2973885853170.05426298053240.29859866342-25.9323276073-12.3290653824-20.7776091066
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 88 through 145 )88 - 1451 - 58
22chain 'A' and (resid 146 through 272 )146 - 27259 - 185
33chain 'A' and (resid 274 through 434 )274 - 434187 - 334

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