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- PDB-7quf: The STK17A (DRAK1) Kinase Domain Bound to CK156 -

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Basic information

Entry
Database: PDB / ID: 7quf
TitleThe STK17A (DRAK1) Kinase Domain Bound to CK156
ComponentsSerine/threonine-protein kinase 17A
KeywordsTRANSFERASE / Kinase Inhibitor Small-molecule binder Macrocycle
Function / homology
Function and homology information


positive regulation of fibroblast apoptotic process / regulation of reactive oxygen species metabolic process / non-specific serine/threonine protein kinase / intracellular signal transduction / nuclear speck / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process ...positive regulation of fibroblast apoptotic process / regulation of reactive oxygen species metabolic process / non-specific serine/threonine protein kinase / intracellular signal transduction / nuclear speck / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ATP binding / nucleus / plasma membrane
Similarity search - Function
Serine/threonine-protein kinase 17A, 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-F8I / Serine/threonine-protein kinase 17A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMathea, S. / Preuss, F. / Chatterjee, D. / Dederer, V. / Kurz, C. / Hanke, T. / Knapp, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Illuminating the Dark: Highly Selective Inhibition of Serine/Threonine Kinase 17A with Pyrazolo[1,5- a ]pyrimidine-Based Macrocycles.
Authors: Kurz, C.G. / Preuss, F. / Tjaden, A. / Cusack, M. / Amrhein, J.A. / Chatterjee, D. / Mathea, S. / Berger, L.M. / Berger, B.T. / Kramer, A. / Weller, M. / Weiss, T. / Muller, S. / Knapp, S. / Hanke, T.
History
DepositionJan 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 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 17A
B: Serine/threonine-protein kinase 17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7994
Polymers63,0082
Non-polymers7912
Water27015
1
A: Serine/threonine-protein kinase 17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9002
Polymers31,5041
Non-polymers3951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase 17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9002
Polymers31,5041
Non-polymers3951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.070, 83.066, 115.836
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Serine/threonine-protein kinase 17A / DAP kinase-related apoptosis-inducing protein kinase 1


Mass: 31504.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK17A, DRAK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UEE5, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-F8I / ~{N}-~{tert}-butyl-7,10-dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.1^{2,6}.0^{17,20}]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxamide


Mass: 395.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 24% PEG3350, 0.2 M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.6→49.27 Å / Num. obs: 21966 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 70.02 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.153 / Net I/σ(I): 22.9
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2158 / CC1/2: 0.908

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Processing

Software
NameVersionClassification
REFMAC7.1.017refinement
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LM0

3lm0


Resolution: 2.6→49.27 Å / SU ML: 0.4263 / Cross valid method: FREE R-VALUE / σ(F): 1.64 / Phase error: 32.3566
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2937 1121 5.1 %
Rwork0.2315 20845 -
obs0.2347 21966 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.82 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 58 15 3842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083907
X-RAY DIFFRACTIONf_angle_d0.95965328
X-RAY DIFFRACTIONf_chiral_restr0.0574630
X-RAY DIFFRACTIONf_plane_restr0.009715
X-RAY DIFFRACTIONf_dihedral_angle_d6.203599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.4151530.342525X-RAY DIFFRACTION99.96
2.72-2.860.34091360.27472591X-RAY DIFFRACTION99.96
2.86-3.040.35121220.27412579X-RAY DIFFRACTION99.93
3.04-3.280.39341360.29032593X-RAY DIFFRACTION100
3.28-3.610.29911430.23432588X-RAY DIFFRACTION99.85
3.61-4.130.26391520.22512583X-RAY DIFFRACTION99.67
4.13-5.20.25031270.19842643X-RAY DIFFRACTION99.43
5.2-49.270.28681520.22032743X-RAY DIFFRACTION99.42
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)
16.07564822671-1.287563155963.138039569542.223181930421.812952657798.450363289050.2156586793350.1807173457760.2832042166340.1307529290070.269770321760.3640622220860.00253689393813-0.25201213333-0.4543652902850.491551448442-0.0005237557162190.04270395016120.412169612450.1734920521390.94395002903-17.838741657312.12109700131.4878790184
22.79989937595-1.3127397779-1.856108714633.413816963741.292308303142.582574524130.138021908350.2414893045490.288833528291-0.1981908667940.0125995421302-0.261884565062-0.0899020620208-0.266231228453-0.1600437871010.440380649964-0.00555537167219-0.008033176575730.3625384577650.06999705595080.686408356739-8.42560376601-0.43048334339829.6431031793
30.9214220807391.96046978708-0.7089253014384.84946798215-1.275860225551.83862260192-0.113300309329-0.2083857814030.4176265783020.182605482914-0.364378851561-1.372830753330.8271468772020.7790736226460.567486650320.637076831770.1938766632120.0003273231790680.61930334660.07372211304780.907883247707-2.36441341783-11.905599273644.2629505923
40.972917077415-2.866465499112.41789596489.51435885593-7.432222021575.95087824442-0.326212744715-0.0372479576560.336533270557-0.324616185063-0.58938829945-0.2946454256951.902287130170.2515821719160.8983430055631.199632559810.2143152018190.2131725844330.73505950970.06319745158950.637758923972-2.43139056113-26.437126790649.6719850826
54.79207051930.0341911170750.272164209373.367794025660.5767740990547.58962218109-0.01767264772330.0114908456015-0.387406320604-0.238581310952-0.234233372027-0.3740310082760.914899387584-0.3884524522240.258441406010.610354816652-0.01535252103470.1517993659920.276891220646-0.0514791504330.684068008718-6.09682297979-21.472457932823.7059782654
63.32571746778-1.466329190260.03830837739165.217944538082.07511023588.40793276233-0.1183230478510.154959735948-0.142546628186-0.158112294564-0.1035067688120.5438422242780.405654518883-0.02886831929190.1943910836260.413034075506-0.1636426930820.05880577825730.618346399628-0.1132195619760.577042799928-37.0919098383-24.185647503143.5731605745
70.6492168137850.00453131405987-0.2369270016321.099334954591.507891180163.02539804588-0.1548821943421.09054976096-1.202762520790.01202060310520.2987746580650.2289463685990.12339372916-1.10081798698-0.04026401506260.4577773215070.0230908563153-0.1162507519320.857644932597-0.1901141233771.01638754952-49.7172632958-22.308883252577.315759858
84.78696991632-0.02167693993920.5174062158847.799079258583.381961296778.408688894690.133930894655-0.3629935072930.735844327833-0.211548272274-0.4751070877370.725553221244-0.517045326174-0.7115937372960.2604534772370.45921154527-0.0201779376949-0.004909881853720.491124837874-0.01279048552910.608805302168-39.9464732946-4.3674012475953.3987385298
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 48 through 93 )AA48 - 931 - 46
22chain 'A' and (resid 94 through 205 )AA94 - 20547 - 153
33chain 'A' and (resid 206 through 226 )AA206 - 226154 - 174
44chain 'A' and (resid 227 through 241 )AA227 - 241175 - 189
55chain 'A' and (resid 242 through 322 )AA242 - 322190 - 270
66chain 'B' and (resid 55 through 219 )BB55 - 2191 - 146
77chain 'B' and (resid 220 through 241 )BB220 - 241147 - 168
88chain 'B' and (resid 242 through 322 )BB242 - 322169 - 249

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