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

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Basic information

Entry
Database: PDB / ID: 9lgn
TitleCrystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 40
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 / SAD / Resolution: 2.03 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 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)64,35511
Polymers63,0322
Non-polymers1,3239
Water1,946108
1
A: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1295
Polymers31,5161
Non-polymers6134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-16 kcal/mol
Surface area13820 Å2
MethodPISA
2
B: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2256
Polymers31,5161
Non-polymers7105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-16 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.450, 110.405, 72.019
Angle α, β, γ (deg.)90.00, 109.97, 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: 31515.887 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-A1EJU / 3-azanyl-4-(7-fluoranyl-2H-indazol-4-yl)-8-methoxy-1H-1,5-naphthyridin-2-one


Mass: 325.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12FN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.03→46.48 Å / Num. obs: 27917 / % possible obs: 88.7 % / Redundancy: 2.9 % / CC1/2: 0.99 / Net I/σ(I): 8
Reflection shellResolution: 2.032→2.283 Å / Num. unique obs: 1421 / CC1/2: 0.399

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
autoPROCdata reduction
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→46.48 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2412 1361 4.88 %
Rwork0.1937 --
obs0.1961 27917 59.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4387 0 83 108 4578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024608
X-RAY DIFFRACTIONf_angle_d0.5086248
X-RAY DIFFRACTIONf_dihedral_angle_d11.011760
X-RAY DIFFRACTIONf_chiral_restr0.038647
X-RAY DIFFRACTIONf_plane_restr0.004823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.10.141330.1413187X-RAY DIFFRACTION20
2.1-2.190.4379260.3283498X-RAY DIFFRACTION20
2.19-2.290.3963390.3012672X-RAY DIFFRACTION20
2.29-2.410.3118530.29181059X-RAY DIFFRACTION24
2.41-2.560.34881210.31442489X-RAY DIFFRACTION56
2.56-2.760.32622140.2934075X-RAY DIFFRACTION91
2.76-3.030.29992100.26884416X-RAY DIFFRACTION99
3.03-3.470.2322250.1974455X-RAY DIFFRACTION99
3.47-4.370.2092280.1574357X-RAY DIFFRACTION98
4.37-100.222420.15994348X-RAY DIFFRACTION96
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)
14.15894.9262-5.08476.8079-6.15078.7798-0.42690.25570.2463-0.42880.51381.17151.4891-2.224-0.12920.7081-0.19460.14330.729-0.11110.9545-23.4574-12.683838.0324
24.5611-0.6603-3.33674.99622.3086.749-0.1052-0.6485-0.30881.2111-0.4505-0.36591.62950.62140.28070.97770.06640.32120.19290.11970.8551-10.2769-21.06834.6616
31.1369-0.5814-2.49274.04421.3725.5597-0.18710.2184-0.2680.25110.02960.32810.9672-0.21270.05490.2325-0.06080.06550.2529-0.06420.3894-12.6912-9.895131.6748
42.41410.62441.1235.27181.35564.3199-0.0526-0.0076-0.3498-0.42630.24790.18470.42010.1743-0.08970.3143-0.0197-0.00530.2432-0.00740.255-1.3558-13.00715.1888
54.68621.38471.03765.99730.93655.3316-0.1662-0.23220.15910.24770.2833-0.4084-0.0050.3706-0.07660.24150.0214-0.00660.276-0.0030.18697.7845-2.732320.7427
60.54931.35050.97954.24353.07452.54240.15980.0543-0.73380.55980.3344-1.87450.40670.7702-0.48730.64680.26440.11060.91090.01230.810718.3104-8.74098.7853
76.8761-2.06410.05855.87421.0557.7763-0.23030.6534-0.3931-1.03450.40930.0750.28810.2073-0.29550.452-0.05490.04040.3414-0.02480.12375.0015-2.38184.9929
82.73671.21272.34274.4237-1.75577.185-0.18320.13620.67470.2446-0.218-0.277-0.60080.60740.22780.1617-0.0015-0.03460.25660.04210.57115.7744-39.080229.8207
92.58050.17040.20115.5754-0.02482.7407-0.07880.1485-0.1059-0.41590.03970.13950.0561-0.16190.08290.26180.02130.01470.24920.00790.138-4.2427-45.346611.3439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 76 through 104 )
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 188 )
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 249 )
5X-RAY DIFFRACTION5chain 'A' and (resid 250 through 316 )
6X-RAY DIFFRACTION6chain 'A' and (resid 317 through 329 )
7X-RAY DIFFRACTION7chain 'A' and (resid 330 through 361 )
8X-RAY DIFFRACTION8chain 'B' and (resid 76 through 188 )
9X-RAY DIFFRACTION9chain 'B' and (resid 189 through 361 )

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