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- PDB-7yaw: Crystal structure of ZAK in complex with compound YH-180 -

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Basic information

Entry
Database: PDB / ID: 7yaw
TitleCrystal structure of ZAK in complex with compound YH-180
ComponentsMitogen-activated protein kinase kinase kinase MLT
KeywordsSTRUCTURAL PROTEIN/INHIBITOR / ZAK / Inhibitor / YH-180 / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / stalled ribosome sensor activity / negative regulation of translation in response to endoplasmic reticulum stress / GCN2-mediated signaling / cell death / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / protein kinase regulator activity / stress-activated protein kinase signaling cascade ...positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / stalled ribosome sensor activity / negative regulation of translation in response to endoplasmic reticulum stress / GCN2-mediated signaling / cell death / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / protein kinase regulator activity / stress-activated protein kinase signaling cascade / positive regulation of programmed cell death / limb development / regulation of mitotic metaphase/anaphase transition / embryonic digit morphogenesis / cellular response to UV-B / pyroptotic inflammatory response / p38MAPK cascade / MAP kinase kinase kinase activity / protein kinase activator activity / stress-activated MAPK cascade / JNK cascade / cytoskeleton organization / DNA damage checkpoint signaling / chromosome segregation / cellular response to gamma radiation / MAPK cascade / ribosome binding / protein autophosphorylation / small ribosomal subunit rRNA binding / cell differentiation / protein phosphorylation / positive regulation of apoptotic process / inflammatory response / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...SAM domain (Sterile alpha motif) / : / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Similarity search - Domain/homology
Chem-IGS / Mitogen-activated protein kinase kinase kinase 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKong, L.L. / Yun, C.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Med.Chem. / Year: 2023
Title: Rational Design of Covalent Kinase Inhibitors by an Integrated Computational Workflow (Kin-Cov).
Authors: Zhou, Y. / Yu, H. / Vind, A.C. / Kong, L. / Liu, Y. / Song, X. / Tu, Z. / Yun, C. / Smaill, J.B. / Zhang, Q.W. / Ding, K. / Bekker-Jensen, S. / Lu, X.
History
DepositionJun 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)143,9858
Polymers141,3504
Non-polymers2,6354
Water7,278404
1
D: Mitogen-activated protein kinase kinase kinase MLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9962
Polymers35,3381
Non-polymers6591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mitogen-activated protein kinase kinase kinase MLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9962
Polymers35,3381
Non-polymers6591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Mitogen-activated protein kinase kinase kinase MLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9962
Polymers35,3381
Non-polymers6591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Mitogen-activated protein kinase kinase kinase MLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9962
Polymers35,3381
Non-polymers6591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.675, 142.772, 179.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35337.504 Da / Num. of mol.: 4
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-IGS / ~{N}-[3-[[5-[1-[2,6-bis(fluoranyl)-3-[(3-phenylphenyl)sulfonylamino]phenyl]-1,2,3-triazol-4-yl]-1~{H}-pyrazolo[3,4-b]pyridin-3-yl]oxy]propyl]propanamide


Mass: 658.678 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H28F2N8O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Magnesium acetate, 0.05 M Sodium acetate pH 5.0, 28% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→31.69 Å / Num. obs: 83627 / % possible obs: 96 % / Redundancy: 20 % / Biso Wilson estimate: 28.13 Å2 / Rpim(I) all: 0.05 / Net I/σ(I): 2
Reflection shellResolution: 2.1→2.15 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 5784 / Rpim(I) all: 0.487

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X5O

5x5o


Resolution: 2.1→31.69 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 4203 5.03 %
Rwork0.2067 79424 -
obs0.2085 83627 95.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.04 Å2 / Biso mean: 35.2366 Å2 / Biso min: 12.12 Å2
Refinement stepCycle: final / Resolution: 2.1→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9472 0 0 404 9876
Biso mean---36.78 -
Num. residues----1164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.120.3107790.2535160658
2.12-2.140.30451030.2625197172
2.14-2.170.3163890.2546224381
2.17-2.20.28241140.2452240387
2.2-2.230.33631230.2423256792
2.23-2.260.25851380.2297254995
2.26-2.290.27541500.231263795
2.29-2.320.24991420.2278267197
2.32-2.360.26761410.2264270199
2.36-2.40.27871500.2255271799
2.4-2.440.27181420.2187273399
2.44-2.480.29011320.2134275099
2.48-2.530.25881510.2114271299
2.53-2.580.23621650.21082717100
2.58-2.640.23511670.2058273999
2.64-2.70.2821610.20132728100
2.7-2.770.23611350.198275599
2.77-2.840.25061690.20012722100
2.84-2.930.25071480.20192749100
2.93-3.020.21641400.19822801100
3.02-3.130.2351230.20452757100
3.13-3.260.2611590.20222762100
3.26-3.40.30931630.2114277899
3.4-3.580.25411510.2055275699
3.58-3.810.23251490.1947275699
3.81-4.10.20421450.1794278399
4.1-4.510.16851480.15277899
4.51-5.160.20761390.1914279198
5.16-6.490.24411360.2276287999
6.49-80.2431510.2114291397

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