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- PDB-6juu: Crystal structure of ZAK in complex with compound 6r -

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Basic information

Entry
Database: PDB / ID: 6juu
TitleCrystal structure of ZAK in complex with compound 6r
ComponentsMitogen-activated protein kinase kinase kinase MLT
KeywordsSTRUCTURAL PROTEIN / ZAK / Inhibitor
Function / homology
Function and homology information


positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / negative regulation of translation in response to endoplasmic reticulum stress / stalled ribosome sensor activity / GCN2-mediated signaling / cell death / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / positive regulation of programmed cell death / regulation of mitotic metaphase/anaphase transition ...positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / negative regulation of translation in response to endoplasmic reticulum stress / stalled ribosome sensor activity / GCN2-mediated signaling / cell death / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / positive regulation of programmed cell death / regulation of mitotic metaphase/anaphase transition / limb development / embryonic digit morphogenesis / cellular response to UV-B / stress-activated protein kinase signaling cascade / protein kinase activator activity / pyroptotic inflammatory response / p38MAPK cascade / MAP kinase kinase kinase activity / stress-activated MAPK cascade / JNK cascade / cytoskeleton organization / DNA damage checkpoint signaling / chromosome segregation / cellular response to gamma radiation / small ribosomal subunit rRNA binding / ribosome binding / protein autophosphorylation / cell differentiation / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-C9R / Mitogen-activated protein kinase kinase kinase 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsKong, L.L. / Yun, C.H.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Design, Synthesis, and Structure-Activity Relationships of 1,2,3-Triazole Benzenesulfonamides as New Selective Leucine-Zipper and Sterile-alpha Motif Kinase (ZAK) Inhibitors.
Authors: Yang, J. / Shibu, M.A. / Kong, L. / Luo, J. / BadrealamKhan, F. / Huang, Y. / Tu, Z.C. / Yun, C.H. / Huang, C.Y. / Ding, K. / Lu, X.
History
DepositionApr 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: 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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase MLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8712
Polymers35,3381
Non-polymers5341
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13700 Å2
Unit cell
Length a, b, c (Å)130.806, 48.509, 42.489
Angle α, β, γ (deg.)90.00, 105.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase MLT


Mass: 35337.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZAK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NYL2, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-C9R / ~{N}-[2,4-bis(fluoranyl)-3-[4-(3-methoxy-1~{H}-pyrazolo[3,4-b]pyridin-5-yl)-1,2,3-triazol-1-yl]phenyl]naphthalene-1-sulfonamide


Mass: 533.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H17F2N7O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.84 Å3/Da / Density % sol: 33.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-Tris pH 6.5, 28% PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 18873 / % possible obs: 99.6 % / Redundancy: 3.3 % / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→1.94 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X5O

5x5o


Resolution: 1.903→39.431 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21
RfactorNum. reflection% reflection
Rfree0.2097 932 4.94 %
Rwork0.1662 --
obs0.1683 18873 92.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.903→39.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 38 103 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072424
X-RAY DIFFRACTIONf_angle_d0.8983286
X-RAY DIFFRACTIONf_dihedral_angle_d7.6711577
X-RAY DIFFRACTIONf_chiral_restr0.056357
X-RAY DIFFRACTIONf_plane_restr0.006411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-3.63930.18241540.16132823X-RAY DIFFRACTION100
1.91-2.00320.24931050.17971879X-RAY DIFFRACTION68
2.0032-2.12870.25761150.17252346X-RAY DIFFRACTION85
2.1287-2.29310.23231220.16792625X-RAY DIFFRACTION96
2.2931-2.52380.21841360.16782758X-RAY DIFFRACTION99
2.5238-2.88890.23271540.17342755X-RAY DIFFRACTION100
2.8889-3.63930.20011460.16162755X-RAY DIFFRACTION100

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