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- PDB-13lv: Structure of PKMYT1 bound to allosteric inhibitor P29-(S) -

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Basic information

Entry
Database: PDB / ID: 13lv
TitleStructure of PKMYT1 bound to allosteric inhibitor P29-(S)
ComponentsMembrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / PKMYT1 / inhibitor / allosteric / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of G2/MI transition of meiotic cell cycle / negative regulation of G2/M transition of mitotic cell cycle / G2/M DNA replication checkpoint / 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 / negative regulation of G2/M transition of mitotic cell cycle / G2/M DNA replication checkpoint / 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 / protein kinase activity / non-specific serine/threonine protein kinase / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / Golgi apparatus / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / 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
: / Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKhamrui, S. / Lazarus, M.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124838 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U01CA271318 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Allosteric Inhibition of PKMYT1 Induces a Unique, Inactive ATP Binding Site Conformation.
Authors: Herrington, N.B. / Khamrui, S. / Zhao, Y. / Lansiquot, C. / Wu, R. / Pandey, G. / Lazarus, M.B. / Schlessinger, A.
History
DepositionMay 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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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)32,5352
Polymers32,2381
Non-polymers2971
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.398, 60.398, 379.379
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 32237.688 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-A1DG4 / (4S)-1-cyclopentyl-4-(4-hydroxyphenyl)-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-b]pyridin-6-one


Mass: 297.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BIS-TRIS, pH 5.5, 3.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 26, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.22→48.335 Å / Num. obs: 14047 / % possible obs: 93.9 % / Redundancy: 21.3 % / CC1/2: 0.998 / Net I/σ(I): 13.7
Reflection shellResolution: 2.22→2.478 Å / Num. unique obs: 702 / CC1/2: 0.611

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
PHASERphasing
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→37.64 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2691 682 4.86 %
Rwork0.2274 --
obs0.2292 14043 65.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 22 3 2246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022320
X-RAY DIFFRACTIONf_angle_d0.4513148
X-RAY DIFFRACTIONf_dihedral_angle_d10.569876
X-RAY DIFFRACTIONf_chiral_restr0.036332
X-RAY DIFFRACTIONf_plane_restr0.003417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.390.29290.3671327X-RAY DIFFRACTION8
2.39-2.630.3022640.3321111X-RAY DIFFRACTION28
2.63-3.010.37231830.29953378X-RAY DIFFRACTION84
3.01-3.80.26232070.2324114X-RAY DIFFRACTION100
3.8-37.640.24462190.2034431X-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)
16.17444.0192-3.18625.8608-3.7815.17350.01540.885-0.00840.14230.56730.50750.3241-1.2408-0.11390.47910.01590.03420.68750.07970.5259-42.238119.5203-2.7465
28.87276.20670.15034.41120.11150.18580.1025-0.4236-0.1528-0.1640.401-0.00431.2726-0.57710.01241.39410.1391-0.10532.38950.54651.8812-46.093425.383-9.943
31.9250.98232.01782.63991.30642.3450.4288-0.3709-0.1814-0.8268-1.25310.80021.0209-0.11910.17911.2746-0.569-0.0471.56010.04231.7118-48.04499.6972-8.8501
47.0885-4.37952.33495.97512.42575.4211-0.1468-0.4928-0.7074-0.58610.6466-0.37852.1566-1.50610.77921.4995-0.64840.31820.708-0.17681.2669-37.6496.542-10.8925
58.1232.0967-0.74299.2254-3.3554.426-0.0963-1.4281-1.46470.2307-1.1911.53381.08741.65310.77111.57790.08720.16061.0069-0.14711.0505-21.172912.1531-12.8111
63.6615-0.02322.04452.46242.47573.9411-0.980.2291-1.0988-1.23770.5129-0.51060.8081-0.04230.03721.5033-0.28390.31620.7961-0.08130.6892-30.369610.9236-14.1773
78.15450.9688-0.27662.32051.67921.3582-0.32630.12030.3955-0.8163-0.10530.064-0.3507-1.54910.92662.3245-0.9759-0.14421.5327-0.3339-0.3743-39.56811.7932-23.0345
84.8391-0.1899-3.71426.2433-1.36813.1893-0.52850.5320.2147-0.64080.3694-0.47210.4774-0.14190.05990.4838-0.14690.02590.34130.05890.3745-30.173922.5865-6.1561
91.40480.2219-3.34150.3097-0.88035.2576-0.95731.0246-0.0364-0.24680.5544-0.07150.8293-1.23190.20530.7281-0.35350.01750.5994-0.01810.4185-29.872718.7704-16.2374
104.0051-0.2933-0.89847.69852.06813.55661.07811.6793-1.7893-0.7486-0.98970.5564-0.17740.72410.11931.30930.07120.08580.852-0.02841.108-10.092813.1084-28.5559
114.5194-1.1107-0.89825.6140.43734.80820.10690.2042-0.3162-0.25460.15710.18320.7431-0.7035-0.05680.4685-0.178-0.08720.46550.03170.2674-19.814427.5017-22.5628
123.7666-0.86891.675.3912.1176.854-0.0119-0.2878-0.41320.2929-0.10830.12710.79670.42120.23590.5283-0.07230.02820.29990.05880.3381-10.801230.008-14.1892
132.83280.6150.04737.9989-1.85212.4311-0.31760.3288-0.117-0.6411-0.2519-1.11120.81210.9370.09610.5710.1024-0.0060.58640.02440.46841.268626.6836-16.7202
145.05856.2669-1.99197.8995-1.91162.9120.2688-2.44210.15151.1364-0.66462.52860.7240.54080.34440.94580.50020.20291.195-0.01071.16553.821223.1395-28.1214
154.6642-1.4081-0.99078.0092-0.46188.93920.05860.36210.5861-0.3512-0.2735-0.35910.259-0.03320.01550.2657-0.09470.01810.34320.14240.2533-9.042636.3434-28.2541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 74:85)
2X-RAY DIFFRACTION2(chain A and resid 86:91)
3X-RAY DIFFRACTION3(chain A and resid 92:101)
4X-RAY DIFFRACTION4(chain A and resid 102:114)
5X-RAY DIFFRACTION5(chain A and resid 115:120)
6X-RAY DIFFRACTION6(chain A and resid 121:130)
7X-RAY DIFFRACTION7(chain A and resid 131:135)
8X-RAY DIFFRACTION8(chain A and resid 136:166)
9X-RAY DIFFRACTION9(chain A and resid 167:196)
10X-RAY DIFFRACTION10(chain A and resid 197:205)
11X-RAY DIFFRACTION11(chain A and resid 206:258)
12X-RAY DIFFRACTION12(chain A and resid 259:302)
13X-RAY DIFFRACTION13(chain A and resid 303:321)
14X-RAY DIFFRACTION14(chain A and resid 322:327)
15X-RAY DIFFRACTION15(chain A and resid 328:361)

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