[English] 日本語
Yorodumi
- PDB-9lgv: Crystal structure of human PKMYT1 protein kinase domain with Naph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lgv
TitleCrystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 11
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 / regulation of cyclin-dependent protein serine/threonine kinase activity / Polo-like kinase mediated events / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / Polo-like kinase mediated events / 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 / 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
: / L(+)-TARTARIC ACID / Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.041 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)65,03612
Polymers63,6162
Non-polymers1,42010
Water3,549197
1
A: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5626
Polymers31,8081
Non-polymers7545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-2 kcal/mol
Surface area13780 Å2
MethodPISA
2
B: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4746
Polymers31,8081
Non-polymers6665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-1 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.570, 110.680, 72.080
Angle α, β, γ (deg.)90.00, 109.34, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 31808.197 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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-A1EJV / 3-azanyl-7-chloranyl-4-(7-fluoranyl-1H-indazol-4-yl)-1H-1,5-naphthyridin-2-one


Mass: 329.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H9ClFN5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 %
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

-
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: Sep 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.04→43.083 Å / Num. obs: 38260 / % possible obs: 82.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.031 / Rrim(I) all: 0.066 / Net I/σ(I): 13.1
Reflection shellResolution: 2.041→2.2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.017 / Num. unique obs: 1914 / Rpim(I) all: 0.542 / Rrim(I) all: 1

-
Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.041→43.08 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1894 4.95 %
Rwork0.1917 --
obs0.1939 38256 82.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.041→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 96 197 4633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034561
X-RAY DIFFRACTIONf_angle_d0.6456165
X-RAY DIFFRACTIONf_dihedral_angle_d12.0621738
X-RAY DIFFRACTIONf_chiral_restr0.042644
X-RAY DIFFRACTIONf_plane_restr0.004815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.041-2.090.223870.2038169X-RAY DIFFRACTION20
2.09-2.150.3109190.282497X-RAY DIFFRACTION40
2.15-2.210.3836790.30291509X-RAY DIFFRACTION48
2.21-2.280.35441430.29492625X-RAY DIFFRACTION83
2.28-2.360.32791660.28583071X-RAY DIFFRACTION97
2.36-2.460.31271900.2553102X-RAY DIFFRACTION100
2.46-2.570.32111410.23133194X-RAY DIFFRACTION100
2.57-2.710.27231670.2343147X-RAY DIFFRACTION100
2.71-2.880.26891560.23193171X-RAY DIFFRACTION100
2.88-3.10.29961530.23483176X-RAY DIFFRACTION100
3.1-3.410.21831530.18343146X-RAY DIFFRACTION100
3.41-3.90.18971640.16823188X-RAY DIFFRACTION100
3.9-4.920.18911750.1443159X-RAY DIFFRACTION100
4.92-100.22061810.17533208X-RAY DIFFRACTION100
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)
14.82091.8222-1.91127.3554-0.27326.4902-0.10150.42790.50950.27050.25811.82630.3117-2.3761-0.27790.5331-0.09210.06760.98170.06971.0095-23.1472-12.633338.3209
21.22840.1191-0.99572.87520.26074.5135-0.1089-0.0038-0.1757-0.0170.11420.2490.5631-0.18360.01930.3112-0.026-0.05810.30080.08360.379-7.4995-13.232626.0127
33.4613-0.1831-1.86085.31422.42682.9689-0.0405-0.55180.44470.24690.04190.1626-0.11280.2975-0.08320.41610.0025-0.01990.4160.07110.40070.4293-0.947126.232
44.24873.54282.57454.16521.75926.4769-0.16850.0697-0.16580.14220.675-0.89920.07621.0864-0.27970.3217-0.00420.0130.4508-0.02290.344111.2718-3.204718.7933
57.2141.07830.70227.0221.99166.3499-0.01150.7001-0.3788-1.07050.4927-0.80930.06381.0311-0.43690.5109-0.04410.08520.5559-0.02260.31368.7529-4.2286.602
64.26311.2192.54455.16180.00196.9086-0.10050.1241-0.11970.4467-0.1552-0.9753-0.15590.63490.22720.3677-0.0419-0.05230.38760.01360.600718.2915-35.424831.8978
72.7799-0.45552.5963.6076-1.57724.80430.01690.2518-0.1251-0.04820.0416-0.4871-0.00960.1641-0.06190.22480.02220.02830.3377-0.0460.420513.644-42.691727.668
83.40440.18250.81393.00430.5842.5158-0.12070.4858-0.1879-0.28390.0726-0.13370.13640.16650.09210.3241-0.00290.04460.3528-0.09540.2529-0.4451-44.031713.9438
91.89861.5706-2.17374.7702-5.80237.1902-0.09110.48430.0767-0.64290.36791.68890.3179-1.2895-0.31690.5158-0.0004-0.12160.6221-0.06440.6688-17.2432-44.809611.6057
104.8457-1.7252-0.71126.5755-1.95965.0850.06630.9435-0.2446-1.4209-0.1328-0.01110.35870.28240.07110.7295-0.0578-0.00390.6996-0.16850.3625-4.5098-49.82861.3623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 77 through 104 )
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 249 )
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 273 )
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 316 )
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 361 )
6X-RAY DIFFRACTION6chain 'B' and (resid 77 through 129 )
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 188 )
8X-RAY DIFFRACTION8chain 'B' and (resid 189 through 301 )
9X-RAY DIFFRACTION9chain 'B' and (resid 302 through 329 )
10X-RAY DIFFRACTION10chain 'B' and (resid 330 through 361 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more