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- PDB-13lx: Structure of PKMYT1 bound to inhibitor P32-(R) -

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Basic information

Entry
Database: PDB / ID: 13lx
TitleStructure of PKMYT1 bound to inhibitor P32-(R)
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: 2.2 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

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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
Water181
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)48.813, 134.247, 113.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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-A1DG5 / (4R)-1-cyclopentyl-4-(3-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.: 1 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
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: 0.919921 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 4, 2025
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919921 Å / Relative weight: 1
ReflectionResolution: 2.2→43.44 Å / Num. obs: 19481 / % possible obs: 100 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.047 / Rrim(I) all: 0.138 / Χ2: 1.01 / Net I/σ(I): 9.5 / Num. measured all: 166067
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 5.009 / Num. measured all: 14468 / Num. unique obs: 1653 / CC1/2: 0.501 / Rpim(I) all: 1.751 / Rrim(I) all: 5.314 / Χ2: 1.02 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.56 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2796 981 5.05 %
Rwork0.2474 --
obs0.249 19435 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 22 1 2244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022299
X-RAY DIFFRACTIONf_angle_d0.5013111
X-RAY DIFFRACTIONf_dihedral_angle_d14.556868
X-RAY DIFFRACTIONf_chiral_restr0.037325
X-RAY DIFFRACTIONf_plane_restr0.003412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.48691480.43712599X-RAY DIFFRACTION100
2.32-2.460.40591360.382581X-RAY DIFFRACTION100
2.46-2.650.39971380.34632603X-RAY DIFFRACTION100
2.65-2.920.38821320.3162618X-RAY DIFFRACTION100
2.92-3.340.26631440.27152616X-RAY DIFFRACTION100
3.34-4.210.27141300.21622676X-RAY DIFFRACTION100
4.21-42.560.22121530.19992761X-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)
14.32613.719-2.70154.8788-4.24714.09320.2820.26890.13270.0935-0.8445-1.3737-1.32021.5441-0.19831.6857-0.48030.18891.2816-0.06021.051319.706536.0589-9.6764
22.23951.6068-1.93176.135-4.48033.5778-0.50970.5085-0.33150.1385-0.4167-2.4702-0.52360.9205-0.08161.70260.06610.36772.0375-0.09171.393924.566530.3034-12.7762
31.24980.2036-1.56790.3169-0.55362.30140.0001-0.92120.2130.1347-0.5248-0.3691-1.0150.7282-0.1232.7764-1.79890.6211.60180.08971.00222.903942.685-23.1862
44.34122.1747-0.43126.092-0.08864.2289-0.12330.62260.8862-1.75940.50171.0191-2.38390.8802-0.57331.7855-0.56760.25030.99820.12040.37519.149933.3625-23.8607
52.98152.32410.11995.40271.26347.5044-0.33910.64480.2442-0.41830.3767-0.3858-1.2144-0.0705-0.25171.3952-0.29090.17830.6067-0.08970.568210.311932.4042-18.1885
62.37790.4787-0.61652.34350.80184.6587-0.41220.16820.5409-0.10220.55970.0457-0.7996-0.0734-0.20790.9088-0.29260.05010.5388-0.0620.44869.509829.3244-4.912
71.69891.2421-1.55943.94720.84343.8229-0.48930.39730.0852-0.70580.7122-0.0101-0.9240.3793-0.11271.1356-0.19520.01640.58230.02690.45096.224923.6738-17.5862
83.66881.87980.68053.22351.47784.5709-0.2330.5863-0.1626-0.50110.21290.04250.79010.35910.00540.8361-0.0018-0.0170.37370.01380.4389-1.18038.5883-12.611
94.49630.3047-0.35234.01610.13786.49280.07120.14350.2539-0.39330.1215-0.438-0.6370.2495-0.12480.8264-0.0557-0.00840.44380.00120.53622.162518.2877-9.9723
102.09321.2629-2.04794.6974-1.33816.57720.0839-0.32140.2058-0.332-0.2159-0.5314-0.68820.5592-0.1541.03060.15250.06070.3820.02550.6211-9.037121.501-2.1606
110.9288-2.36371.46347.0499-1.51159.04830.2417-0.1674-0.33490.8783-0.7982-0.0584-0.4045-0.0377-0.20361.5561-0.1488-0.0640.8048-0.12540.8374-7.609220.5737.4004
122.56711.0273-1.1454.04130.56795.0069-0.17350.3013-0.0239-0.33630.21780.5029-0.5641-0.7917-0.12390.85610.1036-0.06290.4830.02420.5201-14.028615.1833-6.7531
132.82882.1581-0.50014.33530.43189.97030.33120.9305-0.4297-0.55930.18661.4416-0.0361-1.9725-0.08710.9282-0.0362-0.19021.09620.31931.0352-21.63858.4331-9.3746
142.79450.0837-0.75375.0444-0.50974.9672-0.1371-0.1259-0.27410.49720.2052-0.0020.6834-0.3232-0.0070.62990.03550.02870.37890.01530.4891-8.60224.0484-3.7601
158.70663.6117-5.59.9371-6.41681.992-1.73240.6422-2.9299-2.8512-0.5162-1.87120.99192.2187-0.66151.53170.00260.19650.7132-0.12960.81160.384-3.0342-12.8652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 76:84)
2X-RAY DIFFRACTION2(chain A and resid 85:95)
3X-RAY DIFFRACTION3(chain A and resid 96:102)
4X-RAY DIFFRACTION4(chain A and resid 103:130)
5X-RAY DIFFRACTION5(chain A and resid 131:146)
6X-RAY DIFFRACTION6(chain A and resid 147:166)
7X-RAY DIFFRACTION7(chain A and resid 167:201)
8X-RAY DIFFRACTION8(chain A and resid 202:228)
9X-RAY DIFFRACTION9(chain A and resid 229:266)
10X-RAY DIFFRACTION10(chain A and resid 267:278)
11X-RAY DIFFRACTION11(chain A and resid 279:283)
12X-RAY DIFFRACTION12(chain A and resid 284:318)
13X-RAY DIFFRACTION13(chain A and resid 319:326)
14X-RAY DIFFRACTION14(chain A and resid 327:356)
15X-RAY DIFFRACTION15(chain A and resid 357:362)

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