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- PDB-7que: The STK17A (DRAK1) Kinase Domain Bound to CKJB68 -

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Basic information

Entry
Database: PDB / ID: 7que
TitleThe STK17A (DRAK1) Kinase Domain Bound to CKJB68
ComponentsSerine/threonine-protein kinase 17A
KeywordsTRANSFERASE / Kinase Small-molecule binder Inhibitor 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-F7I / Serine/threonine-protein kinase 17A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMathea, S. / Preuss, F. / Chatterjee, D. / Dederer, V. / Kurz, C.G. / Amrhein, J.A. / 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)63,8674
Polymers63,0082
Non-polymers8592
Water46826
1
A: Serine/threonine-protein kinase 17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9342
Polymers31,5041
Non-polymers4291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase 17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9342
Polymers31,5041
Non-polymers4291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.085, 82.776, 116.848
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-F7I / ~{N}-(phenylmethyl)-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: 429.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 19% PEG3350, 0.3 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.34→49.3 Å / Num. obs: 30195 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 66.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.5
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2922 / CC1/2: 0.632 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC7.1.017refinement
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASER7.1.017phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LM0

3lm0


Resolution: 2.4→47.73 Å / SU ML: 0.4557 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 30.3093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 1349 4.82 %
Rwork0.2336 26658 -
obs0.2354 28007 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.55 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3697 0 64 26 3787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00883839
X-RAY DIFFRACTIONf_angle_d1.01655229
X-RAY DIFFRACTIONf_chiral_restr0.0589611
X-RAY DIFFRACTIONf_plane_restr0.0075713
X-RAY DIFFRACTIONf_dihedral_angle_d6.2439596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.44831440.44272621X-RAY DIFFRACTION99.82
2.49-2.590.4441370.35252628X-RAY DIFFRACTION99.96
2.59-2.70.40651150.29682619X-RAY DIFFRACTION100
2.7-2.850.33441090.25842657X-RAY DIFFRACTION100
2.85-3.020.29341200.27052661X-RAY DIFFRACTION99.96
3.02-3.260.31041240.29022667X-RAY DIFFRACTION100
3.26-3.580.28941630.2382618X-RAY DIFFRACTION99.93
3.58-4.10.28591220.21562682X-RAY DIFFRACTION99.93
4.1-5.170.20931560.18552700X-RAY DIFFRACTION100
5.17-47.730.23621590.22182805X-RAY DIFFRACTION99.83
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)
12.52422759158-1.07634122558-0.6317596188724.308783712980.6128316383452.643528862310.1356461594560.07158127631050.325479345584-0.0916342353587-0.0688557991519-0.0951852796903-0.0844903578439-0.0430841219883-0.06464335652340.463998035039-0.011161437840.05144772519020.3326305150140.07810322723630.540847201669-10.95967057623.4903254913730.7570933673
23.50300214337-1.746322739181.587473072758.73440997642-6.236737331584.48282339435-0.244090519462-0.3246169584290.4355848562170.306294639254-0.34732419992-0.8369233196990.8526668064340.576412119640.6824276830540.9746648361740.1929275248080.01614211239940.8015114172180.08487942556730.565784857002-2.49348889447-10.324465675143.8857427754
31.3807321104-2.766725353262.89432213317.27098679646-7.03880034536.94493904711-0.2721260277170.3650137268350.461974640703-0.463911916391-0.26654107418-0.3402819527710.1878337275220.8044009983940.3339319816671.047159421540.2183946508050.1421572972240.4820169367060.002967252582640.484641724976-1.67534372482-25.552499314650.7061049529
44.5614545402-0.2984677230080.6629285811583.34390401594-0.8312217903234.866351881820.03608979126870.189250049499-0.332609084991-0.331765227653-0.185628553706-0.1420605357570.425017553182-0.3141174175410.1955818466380.6288258657320.01290975160250.1423081762950.381214611341-0.07032029616730.541440628168-6.45918877417-21.209937867324.0063120619
54.10586796611-1.99610864575-1.025680495914.299679722312.72177746275.76426809658-0.194160517110.0933969511381-0.4640487910020.0302047732814-0.215375492210.3251272990290.580642024093-0.3459849201350.3867367222930.491519797128-0.1332881655840.04317497394630.4816701824250.03130222026290.451738245457-36.643064066-24.719040090943.1209705078
61.40910197293-1.37913310731-1.019085957291.33739167411.021371720523.49364162982-0.3246340736580.1822234359470.110630018242-0.470548888103-0.1311804349270.08529716725850.8557055334290.4095513290820.6541196095040.604346791858-0.2814612057720.03087421649320.730919400433-0.02641046239830.518620589183-39.2383590024-21.975449467946.3537207132
71.594380625641.93993000341-2.914788550952.485765856-2.889480614648.41943578447-0.1687630398841.16714433071-0.4727677122030.0795767507804-0.1090571772690.114091569839-0.848415053411-1.605267033210.116944603820.6157298605290.0704065799975-0.1190806603550.837891496117-0.1808646889220.712867008144-49.1693036302-21.857243895178.0697896631
84.48622488149-0.862127064497-0.1059221721836.710130901973.354015133278.161119638140.228798026468-0.07289972444180.5189727893040.143631673078-0.3100820691680.529653412774-0.457583499857-0.5781163769660.09406568047660.51923121865-0.0368508003837-0.00944462762420.447169629430.05027819138510.456108524108-40.1166118663-4.959829315654.0647663299
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 205 )AA48 - 2051 - 149
22chain 'A' and (resid 206 through 224 )AA206 - 224150 - 168
33chain 'A' and (resid 225 through 241 )AA225 - 241169 - 185
44chain 'A' and (resid 242 through 322 )AA242 - 322186 - 266
55chain 'B' and (resid 59 through 194 )BB59 - 1941 - 117
66chain 'B' and (resid 195 through 222 )BB195 - 222118 - 139
77chain 'B' and (resid 223 through 241 )BB223 - 241140 - 158
88chain 'B' and (resid 242 through 322 )BB242 - 322159 - 239

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