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- PDB-7mgj: TNNI3K complexed with N-methyl-4-(4-(3-(3-(trifluoromethyl) pheny... -

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Basic information

Entry
Database: PDB / ID: 7mgj
TitleTNNI3K complexed with N-methyl-4-(4-(3-(3-(trifluoromethyl) phenyl) ureido) phenoxy)picolinamide
ComponentsSerine/threonine-protein kinase TNNI3K
KeywordsTRANSFERASE/INHIBITOR / kinase / CARK / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


bundle of His cell to Purkinje myocyte communication / peptidyl-serine autophosphorylation / regulation of cardiac conduction / regulation of cardiac muscle contraction / regulation of heart rate / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity ...bundle of His cell to Purkinje myocyte communication / peptidyl-serine autophosphorylation / regulation of cardiac conduction / regulation of cardiac muscle contraction / regulation of heart rate / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / nucleus / 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-ZFS / Serine/threonine-protein kinase TNNI3K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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

Downloads & links

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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)150,3778
Polymers148,6554
Non-polymers1,7224
Water79344
1
A: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5942
Polymers37,1641
Non-polymers4301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5942
Polymers37,1641
Non-polymers4301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5942
Polymers37,1641
Non-polymers4301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5942
Polymers37,1641
Non-polymers4301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.183, 91.623, 88.154
Angle α, β, γ (deg.)93.330, 117.690, 113.540
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: 37163.852 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-ZFS / N-methyl-4-[4-({[3-(trifluoromethyl)phenyl]carbamoyl}amino)phenoxy]pyridine-2-carboxamide


Mass: 430.380 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H17F3N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.3 M NaK tartrate, 0.1M HEPES pH7

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.912→80 Å / Num. obs: 43990 / % possible obs: 98.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.011 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.95-3.043.20.46436270.871197.4
3.04-3.133.50.38736710.885198.6
3.13-3.253.70.31936290.987198.7
3.25-3.383.90.24236921.039198.9
3.38-3.533.90.20936411.024198.9
3.53-3.7240.14336741.001199.1
3.72-3.9540.11636941.035199.2
3.95-4.2540.09336471.048199.1
4.25-4.6840.08136891.085199.4
4.68-5.3640.07836991.085199.4
5.36-6.7540.06736781.013199.6
6.75-803.90.04536491.002198.3

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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: 2.95→43.96 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 2046 5.05 %
Rwork0.195 38468 -
obs0.1967 40514 90.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.68 Å2 / Biso mean: 53.23 Å2 / Biso min: 23.4 Å2
Refinement stepCycle: final / Resolution: 2.95→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8010 0 124 44 8178
Biso mean--43.86 39.93 -
Num. residues----1044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018346
X-RAY DIFFRACTIONf_angle_d1.33311342
X-RAY DIFFRACTIONf_chiral_restr0.0761274
X-RAY DIFFRACTIONf_plane_restr0.0071473
X-RAY DIFFRACTIONf_dihedral_angle_d12.8712945
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.95-2.97980.28931030.2481197270
2.9798-3.05430.26141330.2424236483
3.0543-3.13690.3211440.2358251190
3.1369-3.22910.2721340.2385278398
3.2291-3.33330.30951450.2283279299
3.3333-3.45240.25981560.2274277999
3.4524-3.59060.36911330.2719257691
3.5906-3.75390.3125650.2867129746
3.7539-3.95170.24471220.2106256190
3.9517-4.19910.21921490.1772282299
4.1991-4.52310.19531530.1544278499
4.5231-4.97770.19751570.153280299
4.9777-5.69660.19871500.17042813100
5.6966-7.17210.22681520.1845280399
7.1721-43.960.15421500.1687280999

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