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- PDB-9lgl: Crystal structure of human PKMYT1 protein kinase domain with Naph... -

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Basic information

Entry
Database: PDB / ID: 9lgl
TitleCrystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 6
ComponentsMembrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
KeywordsTRANSFERASE / inhibitor
Function / homology
Function and homology information


negative regulation of G2/MI transition of meiotic cell cycle / G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of mitotic nuclear division / Cyclin A/B1/B2 associated events during G2/M transition / meiotic cell cycle / G2/M transition of mitotic cell cycle / kinase activity ...negative regulation of G2/MI transition of meiotic cell cycle / G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of mitotic nuclear division / Cyclin A/B1/B2 associated events during G2/M transition / meiotic cell cycle / G2/M transition of mitotic cell cycle / kinase activity / mitotic cell cycle / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / Golgi apparatus / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine/threonine-protein kinase, Cdc2 inhibitor / : / 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
: / Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsXu, Z.H. / Chen, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of Naphthyridinone Derivatives as Selective and Potent PKMYT1 Inhibitors with Antitumor Efficacy.
Authors: Chen, B. / Liu, X. / Mu, T. / Xu, J. / Zhao, D. / Dey, F. / Tang, Y. / Xu, Z. / Yang, J. / Huang, K. / Li, C. / Chen, S. / Zhu, S. / Wang, S. / Yao, X. / Yan, Z. / Tu, Y. / Dai, Y. / Qiu, H. ...Authors: Chen, B. / Liu, X. / Mu, T. / Xu, J. / Zhao, D. / Dey, F. / Tang, Y. / Xu, Z. / Yang, J. / Huang, K. / Li, C. / Chen, S. / Zhu, S. / Wang, S. / Yao, X. / Yan, Z. / Tu, Y. / Dai, Y. / Qiu, H. / Yang, J. / Jiang, T. / Qi, Y. / Li, Y. / Shen, H.C. / Zhu, W. / Tan, X. / Wu, J.
History
DepositionJan 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
B: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3099
Polymers63,4222
Non-polymers8877
Water2,468137
1
A: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2346
Polymers31,7111
Non-polymers5235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0753
Polymers31,7111
Non-polymers3642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.329, 110.933, 73.016
Angle α, β, γ (deg.)90.00, 109.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase / Myt1 kinase


Mass: 31711.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKMYT1, MYT1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q99640, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1EJW / 3-azanyl-7-chloranyl-4-(2-methyl-5-oxidanyl-phenyl)-1H-1,5-naphthyridin-2-one


Mass: 301.728 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.17→68.84 Å / Num. obs: 30286 / % possible obs: 91.8 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.048 / Rrim(I) all: 0.089 / Net I/σ(I): 1.5
Reflection shellResolution: 2.17→2.35 Å / % possible obs: 52.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.798 / Num. measured all: 4293 / Num. unique obs: 1514 / CC1/2: 0.507 / Rpim(I) all: 0.557 / Rrim(I) all: 0.977

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXv1.0refinement
autoPROCdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→58.5 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2342 --
Rwork0.1988 --
obs-30267 91.8 %
Refinement stepCycle: LAST / Resolution: 2.17→58.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 59 137 4458

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