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- PDB-6b5j: TNNI3K complexed with a 4,6-diaminopyrimidine -

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Basic information

Entry
Database: PDB / ID: 6b5j
TitleTNNI3K complexed with a 4,6-diaminopyrimidine
ComponentsSerine/threonine-protein kinase TNNI3K
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


bundle of His cell to Purkinje myocyte communication / regulation of cardiac conduction / regulation of cardiac muscle contraction / 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 conduction / regulation of cardiac muscle contraction / 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 / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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-CV4 / Serine/threonine-protein kinase TNNI3K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsShewchuk, L.M. / Philp, J.
CitationJournal: J. Med. Chem. / Year: 2018
Title: 4,6-Diaminopyrimidines as Highly Preferred Troponin I-Interacting Kinase (TNNI3K) Inhibitors.
Authors: Philp, J. / Lawhorn, B.G. / Graves, A.P. / Shewchuk, L. / Rivera, K.L. / Jolivette, L.J. / Holt, D.A. / Gatto, G.J. / Kallander, L.S.
History
DepositionSep 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 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)141,2478
Polymers139,5534
Non-polymers1,6944
Water59433
1
A: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3122
Polymers34,8881
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3122
Polymers34,8881
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3122
Polymers34,8881
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3122
Polymers34,8881
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.615, 108.193, 92.650
Angle α, β, γ (deg.)90.000, 94.710, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13A
23B
14C
24D
15A
25B
35C
45D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A440 - 614
2112B440 - 614
1122C440 - 614
2122D440 - 614
1132A642 - 730
2132B642 - 730
1144C642 - 730
2144D642 - 730

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999886, 0.013869, 0.005988), (0.013328, 0.996503, -0.082485), (-0.007111, -0.082396, -0.996574)45.746811, 0.65943, 9.21954
3given(-0.171459, 0.499887, 0.84895), (-0.510872, -0.781915, 0.357236), (0.842384, -0.372454, 0.389444)-11.66221, 119.830078, -5.26875
4given(0.126004, 0.402744, -0.906598), (0.547947, -0.790079, -0.274825), (-0.826969, -0.462139, -0.320235)-7.89244, 100.222847, 43.83633

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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 / Plasmid: pFASTBAC / Production host: Baculovirus
References: UniProt: Q59H18, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-CV4 / N-methyl-3-[(6-{[4-(trifluoromethyl)phenyl]amino}pyrimidin-4-yl)amino]benzene-1-sulfonamide


Mass: 423.412 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H16F3N5O2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.06 Å3/Da / Density % sol: 59.84 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 15% tascimate, 0.1M Hepes pH 7, 2% PEG3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.97→92.45 Å / Num. obs: 34379 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.2
Reflection shellResolution: 2.97→3.04 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.57 / Num. unique obs: 1955 / % possible all: 79.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→92.45 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.897 / SU B: 33.171 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 1717 5 %RANDOM
Rwork0.201 ---
obs0.2038 32607 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.58 Å2 / Biso mean: 59.083 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å2-0 Å20.46 Å2
2--3.1 Å20 Å2
3----1.89 Å2
Refinement stepCycle: final / Resolution: 2.97→92.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8135 0 116 33 8284
Biso mean--55.71 40.18 -
Num. residues----1044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198551
X-RAY DIFFRACTIONr_bond_other_d0.0020.028010
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.96911624
X-RAY DIFFRACTIONr_angle_other_deg1.064318412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18751055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16223.77366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.216151384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6171542
X-RAY DIFFRACTIONr_chiral_restr0.0860.21282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219796
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021970
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1514MEDIUM POSITIONAL0.040.5
11A942TIGHT THERMAL4.130.5
11A1514MEDIUM THERMAL3.912
21C1484MEDIUM POSITIONAL0.040.5
21C915TIGHT THERMAL4.890.5
21C1484MEDIUM THERMAL4.892
31A778MEDIUM POSITIONAL0.030.5
31A480TIGHT THERMAL3.010.5
31A778MEDIUM THERMAL3.352
41C1281MEDIUM POSITIONAL0.20.5
41C1281MEDIUM THERMAL3.822
51A29TIGHT THERMAL11.230.5
52B29TIGHT THERMAL11.010.5
53C29TIGHT THERMAL12.530.5
54D29TIGHT THERMAL7.150.5
LS refinement shellResolution: 2.967→3.044 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 86 -
Rwork0.288 1955 -
all-2041 -
obs--79.11 %
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)
13.1113-0.76950.87790.5234-0.11480.4239-0.01230.2727-0.23320.03120.01830.0171-0.05690.0977-0.0060.04390.01720.01610.0508-0.00410.208746.46454.863-3.135
22.77390.60010.35640.40130.09340.2072-0.04-0.0843-0.22580.01770.0239-0.0032-0.05920.01150.01610.03190.00340.03250.0140.03950.1988-0.0454.9968.061
30.2410.05120.11151.62620.93932.48060.0617-0.0143-0.01880.1640.08270.0297-0.36540.182-0.14440.1542-0.03310.0520.046-0.03990.079125.46878.57827.561
40.27-0.01930.01191.9087-0.6711.37590.1001-0.0356-0.0929-0.31730.0260.0168-0.02140.0184-0.12610.1209-0.01290.00310.0389-0.02660.138220.21278.406-23.565
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A445 - 726
2X-RAY DIFFRACTION2B445 - 726
3X-RAY DIFFRACTION3C451 - 726
4X-RAY DIFFRACTION4D452 - 726

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