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- PDB-7mgk: TNNI3K complexed with 1-(3,5-dichloro-4-((6-(methylamino)pyrimidi... -

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Basic information

Entry
Database: PDB / ID: 7mgk
TitleTNNI3K complexed with 1-(3,5-dichloro-4-((6-(methylamino)pyrimidin-4-yl)oxy)phenyl)-3-(3-(trifluoromethyl)phenyl)urea
ComponentsSerine/threonine-protein kinase TNNI3K
KeywordsTRANSFERASE/INHIBITOR / CARK / kinase / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


bundle of His cell to Purkinje myocyte communication / regulation of cardiac muscle contraction / regulation of cardiac conduction / regulation of heart rate / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding ...bundle of His cell to Purkinje myocyte communication / regulation of cardiac muscle contraction / regulation of cardiac conduction / regulation of heart rate / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site ...Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-ZGD / Serine/threonine-protein kinase TNNI3K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsShewchuk, L.M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Identification of Diarylurea Inhibitors of the Cardiac-Specific Kinase TNNI3K by Designing Selectivity Against VEGFR2, p38 alpha , and B-Raf.
Authors: Patterson, J.R. / Graves, A.P. / Stoy, P. / Cheung, M. / Desai, T.A. / Fries, H. / Gatto Jr., G.J. / Holt, D.A. / Shewchuk, L. / Totoritis, R. / Wang, L. / Kallander, L.S.
History
DepositionApr 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 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 1.2Apr 3, 2024Group: 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: Serine/threonine-protein kinase TNNI3K
B: Serine/threonine-protein kinase TNNI3K
C: Serine/threonine-protein kinase TNNI3K
D: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,4428
Polymers139,5534
Non-polymers1,8894
Water25214
1
A: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3612
Polymers34,8881
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3612
Polymers34,8881
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3612
Polymers34,8881
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3612
Polymers34,8881
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.673, 75.072, 95.235
Angle α, β, γ (deg.)83.280, 85.950, 74.790
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Serine/threonine-protein kinase TNNI3K / Cardiac ankyrin repeat kinase / Cardiac troponin I-interacting kinase / TNNI3-interacting kinase


Mass: 34888.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNI3K, CARK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q59H18, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-ZGD / N-(3,5-dichloro-4-{[6-(methylamino)pyrimidin-4-yl]oxy}phenyl)-N'-[3-(trifluoromethyl)phenyl]urea


Mass: 472.248 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H14Cl2F3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 15% tacsimate, and 2% PEG3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 32581 / % possible obs: 76.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 67.19 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.04 / Net I/σ(I): 10.2 / Num. measured all: 107295
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.8-2.91.30.6383400.90318
2.9-3.021.60.50110881.054125.7
3.02-3.1520.45324431.066157.5
3.15-3.322.60.34934881.098182.6
3.32-3.5330.27541321.111196.6
3.53-3.83.50.17942241.076198.7
3.8-4.183.70.12541911.086199
4.18-4.793.80.08442160.95199.3
4.79-6.033.80.08942271.05199.4
6.03-503.80.05142320.961199.7

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Processing

Software
NameVersionClassification
PHENIXdev_1148refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished structure

Resolution: 3.1→41.508 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 1469 4.96 %
Rwork0.1963 28159 -
obs0.1984 29628 95.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.29 Å2 / Biso mean: 58.22 Å2 / Biso min: 26.58 Å2
Refinement stepCycle: final / Resolution: 3.1→41.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8029 0 124 14 8167
Biso mean--56.48 43.02 -
Num. residues----1046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058362
X-RAY DIFFRACTIONf_angle_d0.88211368
X-RAY DIFFRACTIONf_chiral_restr0.0551277
X-RAY DIFFRACTIONf_plane_restr0.0041436
X-RAY DIFFRACTIONf_dihedral_angle_d12.982941
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.21080.35061100.2637216573
3.2108-3.33930.2821250.2458260789
3.3393-3.49120.32231400.2374288097
3.4912-3.67510.26291540.2091293998
3.6751-3.90520.28241680.1868288399
3.9052-4.20650.22241370.178293699
4.2065-4.62930.20971660.1532294599
4.6293-5.2980.2071600.1763293499
5.298-6.67040.25921420.2152293299
6.6704-41.5080.19981670.1983293899

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