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- PDB-13lw: Structure of PKMYT1 bound to inhibitor P32-(S) -

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Basic information

Entry
Database: PDB / ID: 13lw
TitleStructure of PKMYT1 bound to inhibitor P32-(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: 1.95 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
Water23413
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)48.684, 134.408, 114.476
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-A1DG6 / (4S)-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.: 13 / 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: 57.65 %
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: 1.95→43.58 Å / Num. obs: 27783 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Χ2: 0.99 / Net I/σ(I): 10.5 / Num. measured all: 197043
Reflection shellResolution: 1.95→2 Å / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 2.835 / Num. measured all: 14039 / Num. unique obs: 1901 / CC1/2: 0.431 / Rpim(I) all: 1.112 / Rrim(I) all: 3.049 / 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: 1.95→43.58 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1365 4.93 %
Rwork0.2249 --
obs0.226 27710 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→43.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 22 13 2249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022291
X-RAY DIFFRACTIONf_angle_d0.5173100
X-RAY DIFFRACTIONf_dihedral_angle_d13.904864
X-RAY DIFFRACTIONf_chiral_restr0.038324
X-RAY DIFFRACTIONf_plane_restr0.003411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.48681460.42182563X-RAY DIFFRACTION100
2.02-2.10.35951320.3772600X-RAY DIFFRACTION99
2.1-2.20.35591340.33742565X-RAY DIFFRACTION99
2.2-2.310.32231370.30952615X-RAY DIFFRACTION99
2.31-2.460.27341370.27262603X-RAY DIFFRACTION100
2.46-2.650.29271570.27332613X-RAY DIFFRACTION100
2.65-2.910.3731280.29162635X-RAY DIFFRACTION100
2.91-3.330.27691160.25582680X-RAY DIFFRACTION100
3.33-4.20.22341340.19262684X-RAY DIFFRACTION100
4.2-43.580.18491440.17362787X-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)
12.82413.06610.19428.96210.65420.0480.25030.3699-0.4702-0.7808-0.9258-1.1713-1.6841.4171-0.19071.6991-0.57410.14461.3578-0.16360.86420.036637.4186-9.2535
22.56512.2829-2.55714.1956-4.56668.5691-0.33711.2484-0.2286-0.1838-0.2538-1.8434-0.75841.8782-0.02281.8662-0.17680.32061.88470.02391.486724.503630.3945-12.7406
33.7726-0.3033-3.18170.17790.38272.7732-0.0859-0.09210.3868-0.5351-0.3129-0.3865-1.24740.67320.06912.4048-1.20730.23841.844-0.02941.112222.659342.866-23.4054
43.76282.82910.07025.87480.13364.9709-0.22250.28061.0279-2.34340.37410.9065-2.51371.1864-0.88861.5022-0.70250.25651.10990.17120.1949.102433.4858-23.9654
52.92912.40550.06446.76671.70428.0262-0.22710.41370.1452-0.91830.7178-0.5711-1.57790.8142-0.22021.192-0.36480.10330.7154-0.00770.538510.210832.3912-18.2442
62.54190.9979-0.04162.37381.64235.5272-0.02170.22720.0243-0.1060.00060.6509-0.92260.1568-0.20280.757-0.27840.00730.5516-0.03190.40319.570929.5633-4.9177
72.72360.8167-1.10924.33630.25744.5506-0.38260.4387-0.0747-0.62570.6772-0.247-0.84470.5934-0.09610.809-0.22150.04740.6131-0.00940.3376.207423.7075-17.678
83.68362.11760.71834.27650.28235.4463-0.36410.5819-0.2866-0.50190.39920.04340.22930.2853-0.02140.6548-0.0056-0.00030.3901-0.00140.4206-1.15678.5361-12.6846
95.82160.65490.90974.6272-1.30196.70480.02680.24440.25220.0422-0.0673-0.2421-0.57460.3212-0.12870.6408-0.0731-0.00380.3790.01310.41912.133419.0024-8.7424
103.9871.0269-1.08925.0594-2.01929.3479-0.5589-0.33180.6110.80110.4767-0.6114-0.7237-0.0187-0.13480.85140.1879-0.01220.40480.01680.5181-9.415621.6521-2.0555
116.923-4.44432.88627.7328-1.01449.58430.3691-0.87050.39090.63090.12580.177-0.90640.1718-0.17540.94970.0175-0.04650.6014-0.1410.8812-7.386220.68417.5033
123.49450.7606-0.79474.66150.32245.7578-0.0740.3547-0.0391-0.18630.130.4899-0.2974-0.6673-0.12940.62520.0631-0.02070.47820.05270.4687-13.953115.2081-6.7612
133.60332.63120.54493.9049-0.0171.9417-0.720.61050.4156-0.85930.38860.75230.1822-1.8079-0.12890.9748-0.0281-0.06031.41820.24851.0856-21.60768.5512-9.2595
143.120.6856-0.60674.75910.17365.9816-0.1996-0.0502-0.1010.33430.19540.01170.4173-0.2593-0.01790.57850.00210.02110.36180.04220.4206-8.5724.0245-3.7697
157.52612.163-2.6277.8815-4.81047.3796-0.76111.3074-1.5626-2.01040.0045-2.01630.87572.6004-0.18711.3515-0.11850.29540.7975-0.13080.65390.5055-2.8645-12.6595
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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