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- PDB-9m6p: Discovery of a bifunctional PKMYT1-targeting PROTAC empowered by ... -

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Basic information

Entry
Database: PDB / ID: 9m6p
TitleDiscovery of a bifunctional PKMYT1-targeting PROTAC empowered by AI-generation
ComponentsMembrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
KeywordsPROTEIN BINDING / PKMYT1 / inhibitor / crystal
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 / cytoplasm / cytosol
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
: / PHOSPHATE ION / Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.383 Å
AuthorsYazhou, W. / Chao, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Discovery of a bifunctional PKMYT1-targeting PROTAC empowered by AI-generation
Authors: Wang, Y. / Ding, X.
History
DepositionMar 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
BBB: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8827
Polymers68,9962
Non-polymers8865
Water55831
1
AAA: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
BBB: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules

AAA: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
BBB: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules

AAA: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
BBB: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,64721
Polymers206,9896
Non-polymers2,65815
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2_545-y,x-y-1,z1
point symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)127.927, 127.927, 184.655
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11AAA-518-

HOH

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Components

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


Mass: 34498.133 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 (bacteria)
References: UniProt: Q99640, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1EMX / 2,4-dimethyl-3-[2-(2-methylpyrimidin-5-yl)-1~{H}-pyrrolo[2,3-b]pyridin-5-yl]phenol


Mass: 330.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#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.: 31 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: SM5-E1+30%Gly

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.88→100 Å / Num. obs: 24659 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 10
Reflection shellResolution: 1.88→1.92 Å / Rmerge(I) obs: 1.213 / Num. unique obs: 21329

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.383→95.001 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.861 / SU B: 15.517 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.518
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 652 5.078 %RANDOM
Rwork0.2028 12187 --
all0.207 ---
obs-12839 54.688 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 62.015 Å2
Baniso -1Baniso -2Baniso -3
1-0.028 Å20.014 Å2-0 Å2
2--0.028 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.383→95.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 61 31 4433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134507
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174244
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.6626101
X-RAY DIFFRACTIONr_angle_other_deg1.1321.5859769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2085554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63320.769247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14715744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8171542
X-RAY DIFFRACTIONr_chiral_restr0.0490.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021064
X-RAY DIFFRACTIONr_nbd_refined0.2250.2970
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.24093
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22123
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22233
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2121
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.231
X-RAY DIFFRACTIONr_nbd_other0.2240.2106
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2670.26
X-RAY DIFFRACTIONr_mcbond_it3.7716.4382228
X-RAY DIFFRACTIONr_mcbond_other3.7546.4382227
X-RAY DIFFRACTIONr_mcangle_it6.1039.6462778
X-RAY DIFFRACTIONr_mcangle_other6.1059.6472779
X-RAY DIFFRACTIONr_scbond_it3.6886.7752279
X-RAY DIFFRACTIONr_scbond_other3.6816.7782272
X-RAY DIFFRACTIONr_scangle_it6.06410.0173323
X-RAY DIFFRACTIONr_scangle_other6.06710.023312
X-RAY DIFFRACTIONr_lrange_it9.21473.5174989
X-RAY DIFFRACTIONr_lrange_other9.21473.5144990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.383-2.4440.56930.26320.27616930.3870.6812.06730.257
2.444-2.5110.58750.305700.32216900.4840.6834.43790.307
2.511-2.5840.359110.3181210.32216180.7630.7398.15820.3
2.584-2.6640.414130.311780.31816010.7170.74911.930.305
2.664-2.7510.293190.3112620.3115200.7020.76718.48680.305
2.751-2.8470.348240.2893440.29314930.7980.78124.64840.278
2.847-2.9550.345280.2714560.27514140.7540.81234.22910.245
2.955-3.0750.318290.2726070.27413940.8110.81445.62410.257
3.075-3.2120.363410.269270.26513400.7750.82872.23880.233
3.212-3.3680.322570.24811460.25112430.8220.85196.7820.218
3.368-3.550.308560.22811740.23212340.8720.88799.67580.204
3.55-3.7650.276600.20210750.20611350.8780.9121000.175
3.765-4.0250.267520.17410380.17910900.8980.9321000.15
4.025-4.3470.249490.1699590.17310080.9290.9431000.153
4.347-4.7610.262540.1648790.1699330.9240.9491000.147
4.761-5.3210.362400.198110.1978510.8760.9351000.173
5.321-6.1410.318380.2167110.227490.8830.9221000.198
6.141-7.5130.218380.1996140.26520.9250.9231000.184
7.513-10.5920.207190.1554920.1575110.9480.9741000.161
10.592-95.0010.363160.2572900.2623070.910.95499.67430.271

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