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- PDB-5x5o: Crystal structure of ZAK in complex with compound D2829 -

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Basic information

Entry
Database: PDB / ID: 5x5o
TitleCrystal structure of ZAK in complex with compound D2829
ComponentsMitogen-activated protein kinase kinase kinase MLT
KeywordsTRANSFERASE / ZAK / kinase / 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 / stress-activated protein kinase signaling cascade / positive regulation of programmed cell death ...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 / stress-activated protein kinase signaling cascade / positive regulation of programmed cell death / regulation of mitotic metaphase/anaphase transition / limb development / embryonic digit morphogenesis / cellular response to UV-B / 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 / MAPK cascade / ribosome binding / small ribosomal subunit rRNA binding / protein autophosphorylation / cell differentiation / inflammatory response / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / RNA binding / ATP binding / nucleus / cytoplasm / cytosol
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-7Z0 / Mitogen-activated protein kinase kinase kinase 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.868 Å
AuthorsDai, Y.B. / Zhao, P. / Yun, C.H.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation of China31270769 China
National Basic Research Program of China2012CB917202 China
Ministry of Science and Technology of ChinaNCET-12-0013 China
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure Based Design of N-(3-((1H-Pyrazolo[3,4-b]pyridin-5-yl)ethynyl)benzenesulfonamides as Selective Leucine-Zipper and Sterile-alpha Motif Kinase (ZAK) Inhibitors.
Authors: Chang, Y. / Lu, X. / Shibu, M.A. / Dai, Y.B. / Luo, J. / Zhang, Y. / Li, Y. / Zhao, P. / Zhang, Z. / Xu, Y. / Tu, Z.C. / Zhang, Q.W. / Yun, C.H. / Huang, C.Y. / Ding, K.
History
DepositionFeb 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Mitogen-activated protein kinase kinase kinase MLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8572
Polymers35,3381
Non-polymers5191
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13410 Å2
Unit cell
Length a, b, c (Å)131.057, 48.501, 42.625
Angle α, β, γ (deg.)90.00, 105.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-590-

HOH

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase MLT / Human cervical cancer suppressor gene 4 protein / HCCS-4 / Leucine zipper- and sterile alpha motif- ...Human cervical cancer suppressor gene 4 protein / HCCS-4 / Leucine zipper- and sterile alpha motif-containing kinase / MLK-like mitogen-activated protein triple kinase / Mixed lineage kinase-related kinase / MRK / Sterile alpha motif- and leucine zipper-containing kinase AZK


Mass: 35337.504 Da / Num. of mol.: 1 / Fragment: ZAK kinase domain (UNP RESIDUES 5-309)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZAK, MLTK, HCCS4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NYL2, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-7Z0 / N-[2,4-bis(fluoranyl)-3-[2-(3-methoxy-1H-pyrazolo[3,4-b]pyridin-5-yl)ethynyl]phenyl]-3-bromanyl-benzenesulfonamide


Mass: 519.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H13BrF2N4O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.85 Å3/Da / Density % sol: 33.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Trimethylamine N-oxide dehydrate, 0.1 M Tris, 20% w/v Polyethylene glycol monomethyl ether 2000, pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 300K / Detector: CMOS / Date: Jan 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 20966 / % possible obs: 97.2 % / Redundancy: 10.3 % / Net I/σ(I): 18

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.868→45.277 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 1081 5.16 %
Rwork0.1898 --
obs0.1918 20934 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.868→45.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 32 140 2493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082417
X-RAY DIFFRACTIONf_angle_d0.9423276
X-RAY DIFFRACTIONf_dihedral_angle_d14.8211440
X-RAY DIFFRACTIONf_chiral_restr0.062358
X-RAY DIFFRACTIONf_plane_restr0.006411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8676-1.95260.32031110.23242175X-RAY DIFFRACTION85
1.9526-2.05550.30191220.22722414X-RAY DIFFRACTION95
2.0555-2.18430.26911380.2052522X-RAY DIFFRACTION99
2.1843-2.35290.26681300.18842525X-RAY DIFFRACTION100
2.3529-2.58970.2251570.18622524X-RAY DIFFRACTION99
2.5897-2.96440.20881400.18332534X-RAY DIFFRACTION100
2.9644-3.73460.20131320.17822568X-RAY DIFFRACTION99
3.7346-45.29060.20671510.18672591X-RAY DIFFRACTION99

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