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- PDB-8zu2: Crystal Structure of Human Myt1 Kinase domain Bounded with compound 8g -

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Basic information

Entry
Database: PDB / ID: 8zu2
TitleCrystal Structure of Human Myt1 Kinase domain Bounded with compound 8g
ComponentsMembrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
KeywordsGENE REGULATION / protein kinase
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
: / GLYCINE / Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79888582046 Å
AuthorsZhang, Z.M. / Zhou, Z.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Structure-Based Drug Design of 2-Amino-[1,1'-biphenyl]-3-carboxamide Derivatives as Selective PKMYT1 Inhibitors for the Treatment of CCNE1 -Amplified Breast Cancer.
Authors: Wang, C. / Fang, Y. / Zhou, Z. / Liu, Z. / Feng, F. / Wan, X. / Li, Y. / Liu, S. / Ding, J. / Zhang, Z.M. / Xie, H. / Lu, X.
History
DepositionJun 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2183
Polymers31,7111
Non-polymers5072
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.669, 58.555, 99.271
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-852-

HOH

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKMYT1, MYT1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99640, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-A1D85 / 2-azanyl-5-[2-(1,4-diazepan-1-yl)pyridin-4-yl]-3-(2,6-dimethyl-3-oxidanyl-phenyl)benzamide


Mass: 431.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H29N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.8 M Ammonium sulfate,100 mM Sodium citrate,pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.798→49.64 Å / Num. obs: 30816 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.7021685186 Å2 / CC1/2: 0.987 / Net I/σ(I): 5.3
Reflection shellResolution: 1.799→1.863 Å / Num. unique obs: 30816 / CC1/2: 0.987

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
PHENIX1.9_1692+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P1A

3p1a


Resolution: 1.79888582046→49.6355 Å / SU ML: 0.182018053325 / Cross valid method: FREE R-VALUE / σ(F): 1.36279144675 / Phase error: 20.7130112894
RfactorNum. reflection% reflection
Rfree0.221898753519 2004 6.50374841788 %
Rwork0.178076821488 28809 -
obs0.180922103115 30813 99.8930169228 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.1737194985 Å2
Refinement stepCycle: LAST / Resolution: 1.79888582046→49.6355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 5 304 2457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006488157234572205
X-RAY DIFFRACTIONf_angle_d1.004887376242983
X-RAY DIFFRACTIONf_chiral_restr0.0439254941877311
X-RAY DIFFRACTIONf_plane_restr0.00514518656409391
X-RAY DIFFRACTIONf_dihedral_angle_d14.0209563075820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7989-1.84390.2650220685071390.2053520886651997X-RAY DIFFRACTION99.3488372093
1.8439-1.89370.2416402047331410.1947496697732020X-RAY DIFFRACTION99.953746531
1.8937-1.94950.2324217983681430.1852626097512014X-RAY DIFFRACTION100
1.9495-2.01240.2465918106231400.1801854621282038X-RAY DIFFRACTION100
2.0124-2.08430.2149285369251460.1709318155012025X-RAY DIFFRACTION99.9539594843
2.0843-2.16780.2195417038661340.1683691055612056X-RAY DIFFRACTION100
2.1678-2.26640.2285207313621520.173026569362024X-RAY DIFFRACTION99.9540652274
2.2664-2.38590.2275039369031370.173154695742035X-RAY DIFFRACTION99.9539806719
2.3859-2.53540.2005532457381390.1824537065692070X-RAY DIFFRACTION100
2.5354-2.73110.2276175540531440.179920836752051X-RAY DIFFRACTION99.9544626594
2.7311-3.00590.2396643427131450.1869675342212068X-RAY DIFFRACTION99.9548328817
3.0059-3.44080.2092960534511470.1687663522752082X-RAY DIFFRACTION99.9551569507
3.4408-4.33470.1877676189831430.1574469205622113X-RAY DIFFRACTION99.9114260407
4.3347-49.630.2439259864861540.1975814838962216X-RAY DIFFRACTION99.6216897856
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)
12.15876994355-1.273613397961.246321678532.03318869073-0.6586432671243.05098213506-0.388092683187-0.07407382887340.1768764308920.515864047020.108204153819-0.7523954510450.03553756159640.4199283876750.04811350268670.2626569389480.106477865245-0.06891160863240.271860151774-0.05319859470940.32415825862626.5547440575-29.4385054393-15.0035186422
21.01699624412-0.1101947270870.07759974224451.391052439840.6638565135971.8482702769-0.143066620824-0.12814797527-0.0686039776280.5644876260040.177794597919-0.256724082940.4775687969590.311125286326-0.04546881235970.185581100640.0765081381011-0.09110793364820.177020673707-0.009609658202510.1553833749516.0060158533-23.3494479069-7.26787792792
30.887651196577-0.395293186536-0.4499390875897.071274850820.9863097897771.46872215255-0.0763374799645-0.0831386996650.00620808735857-0.1291175932070.06793694114490.0733344981026-0.111919113687-0.0177032935465-0.01530581449610.09964335160130.0335192733611-0.02391331082730.156825743791-0.001449590419980.15661639545312.3534444094-25.0961162744-24.0806400386
41.21597793522-0.6165095780780.72263827612.12327348855-0.1659727841591.01294199197-0.248373602451-0.04638213504530.199804475550.2569271281090.202024072432-0.254412329458-0.02071530785990.01181805766270.02072966988120.0816989399429-0.0197033445501-0.02541311486990.1095816562990.01119802632510.08950633655267.92544354715-10.1415957074-14.2881258646
53.710722218650.1771265254370.117796014422.64379339616-0.07107490945773.0460954746-0.07001542439410.03500164122490.03885492438820.02929918584910.0297732716153-0.1403418439330.04731671041610.217618677278-0.02960969603710.071542779986-0.00151503478034-0.02095395910330.09301012839220.01984896144490.08966423688254.84161979223-11.7996176428-18.2346055059
62.502847588940.540657041153-0.7348908877732.62824442655-0.2860256980273.13887339098-0.254411194188-0.00328910191124-0.517932842821-0.206567888706-0.00990726468854-0.1276756507750.4534390997320.268835845844-0.03762849603790.172882217327-0.007556699827640.008970866825410.1415441268790.01027485780180.231505480872-5.4603905388-17.8105206941-26.7176926175
72.510505674140.1454281827640.388319839551.912575498770.3581805964211.48728444611-0.0159445002324-0.1935263840570.03141373391020.198575311334-0.04033003291540.137178120635-0.0173159262693-0.114101677730.07840845394780.0983101804710.00913805300304-0.007911467341080.09599372184190.002492275850920.103324813033-12.4958868617-5.86514572052-18.466697066
83.26614859881-0.253182796825-0.7783290551122.95382198179-0.2664869945092.15428326436-0.0656179035632-0.007290694515380.396541262069-0.1290540042280.06542976045730.0760421017161-0.208586245881-0.1013401830920.07749817578220.114568391922-0.00856863149203-0.02159486568660.09585523875530.05963273139620.138060880915-3.568926403181.26294446803-27.1382930107
92.000050108851.99989724931.999966293722.000031236352.000069378812.00007742371-2.303804681710.662678752937-14.8014918635-4.209332377341.79125540994-16.2211644067.803444995671.773152764070.4842130393310.7312954712970.197750341559-0.01139119632390.51014277996-0.2123178948990.694061339129-8.366291074539.1601113055-24.5769417875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 75 through 104 )
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 147 )
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 164 )
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 227 )
5X-RAY DIFFRACTION5chain 'A' and (resid 228 through 257 )
6X-RAY DIFFRACTION6chain 'A' and (resid 258 through 284 )
7X-RAY DIFFRACTION7chain 'A' and (resid 285 through 339 )
8X-RAY DIFFRACTION8chain 'A' and (resid 340 through 361 )
9X-RAY DIFFRACTION9chain 'A' and (resid 501 through 501 )

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