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- PDB-8zul: Crystal Structure of Human Myt1 Kinase domain Bounded with compound 8m -

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Basic information

Entry
Database: PDB / ID: 8zul
TitleCrystal Structure of Human Myt1 Kinase domain Bounded with compound 8m
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
: / Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80026162696 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 9, 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)32,1292
Polymers31,7111
Non-polymers4181
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.801, 55.834, 58.633
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-700-

HOH

21A-707-

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-A1D84 / 2-azanyl-5-[2-[(3~{R})-3-azanylpyrrolidin-1-yl]pyridin-4-yl]-3-(2,6-dimethyl-3-oxidanyl-phenyl)benzamide


Mass: 417.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→48.73 Å / Num. obs: 31010 / % possible obs: 99.75 % / Redundancy: 8.7 % / Biso Wilson estimate: 24.3348878612 Å2 / CC1/2: 0.488 / Net I/σ(I): 2.8
Reflection shellResolution: 1.8→1.865 Å / Num. unique obs: 31010 / CC1/2: 0.488

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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: 1.80026162696→48.7268528655 Å / SU ML: 0.173597198741 / Cross valid method: FREE R-VALUE / σ(F): 1.36879648888 / Phase error: 22.5700514482
RfactorNum. reflection% reflection
Rfree0.21916359869 1986 6.4066582793 %
Rwork0.185853061644 29013 -
obs0.187966331096 30999 99.7169234728 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.6865695572 Å2
Refinement stepCycle: LAST / Resolution: 1.80026162696→48.7268528655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 0 210 2386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052579559032229
X-RAY DIFFRACTIONf_angle_d1.213235143663019
X-RAY DIFFRACTIONf_chiral_restr0.0634629364473317
X-RAY DIFFRACTIONf_plane_restr0.00634847394285396
X-RAY DIFFRACTIONf_dihedral_angle_d13.3767709317822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.84530.3233954734341300.2410677016881999X-RAY DIFFRACTION97.3479652492
1.8453-1.89520.2491530421161460.2035632902792025X-RAY DIFFRACTION99.9539594843
1.8952-1.95090.2397034032741390.1916451073272046X-RAY DIFFRACTION99.9542543458
1.9509-2.01390.2381226415581400.1927861116822048X-RAY DIFFRACTION100
2.0139-2.08590.2691075894431360.1888142794872056X-RAY DIFFRACTION100
2.0859-2.16940.2546676181481490.1911369849762059X-RAY DIFFRACTION100
2.1694-2.26810.2195556870211410.1851252431962052X-RAY DIFFRACTION100
2.2681-2.38770.2251343041061370.1851198149582050X-RAY DIFFRACTION100
2.3877-2.53730.2654088310831470.1894671441632087X-RAY DIFFRACTION100
2.5373-2.73320.2246707898831420.190850854962046X-RAY DIFFRACTION100
2.7332-3.00820.2533249634791450.1981067920392090X-RAY DIFFRACTION100
3.0082-3.44340.2228131736521420.1811531611722107X-RAY DIFFRACTION100
3.4434-4.33790.1618137928611420.162132X-RAY DIFFRACTION99.9121265378
4.3379-48.720.1929262136841500.1913052223992216X-RAY DIFFRACTION98.9130434783
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)
11.40318473112-0.1916556403610.8207778566310.376128972114-0.4769500379352.27171417532-0.04011225393810.2765853024910.259839325052-0.0166877557905-0.04053516950110.0170213971014-0.2695634591610.2281701572140.05321602431440.244829684426-0.0546367228347-0.02139431464780.2037955182220.04428443911530.251086498492-13.40386977318.2985613936-23.9964719301
21.65790901240.594569188239-0.441460375012.602493033940.1743726190151.745680021690.08878937414610.04195007835730.0306757435602-0.108375332039-0.121742052862-0.0580736874721-0.08828533196990.08609707656310.01294356514660.139427248604-0.01335259599480.01983716712420.144578075778-0.0150470292060.141956667322-18.34173981961.15751734649-10.2913710407
30.8450940986770.248675781139-0.04769195820321.714739045830.4781549245231.638534847850.0382592475998-0.0474247417635-0.09211006045050.107438383297-0.0462266004555-0.1588940378940.08898716236940.06965620704460.01110100946150.181122989138-0.0229378194434-0.00459528328970.1764261190870.005926760776030.169510409165-21.0800134159-9.72413418558-3.78611184212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 75 through 188 )
2X-RAY DIFFRACTION2chain 'A' and (resid 189 through 284 )
3X-RAY DIFFRACTION3chain 'A' and (resid 285 through 361 )

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