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- PDB-7ukz: CDK11 in complex with small molecule inhibitor OTS964 -

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Basic information

Entry
Database: PDB / ID: 7ukz
TitleCDK11 in complex with small molecule inhibitor OTS964
ComponentsCyclin-dependent kinase 11B
KeywordsTRANSFERASE/Inhibitor / Kinase / Inhibitor / TRANSFERASE / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


regulation of mRNA processing / regulation of centrosome cycle / regulation of RNA splicing / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / Recruitment of mitotic centrosome proteins and complexes / regulation of cell growth / mitotic cell cycle / regulation of apoptotic process ...regulation of mRNA processing / regulation of centrosome cycle / regulation of RNA splicing / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / Recruitment of mitotic centrosome proteins and complexes / regulation of cell growth / mitotic cell cycle / regulation of apoptotic process / protein phosphorylation / protein kinase activity / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / regulation of DNA-templated transcription / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Cyclin-dependent kinase 11/PITSLRE, catalytic domain / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
OTS964 / Cyclin-dependent kinase 11B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsKelso, S. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-143277 Canada
CitationJournal: Structure / Year: 2022
Title: Crystal structure of the CDK11 kinase domain bound to the small-molecule inhibitor OTS964.
Authors: Kelso, S. / O'Brien, S. / Kurinov, I. / Angers, S. / Sicheri, F.
History
DepositionApr 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase 11B
B: Cyclin-dependent kinase 11B
C: Cyclin-dependent kinase 11B
D: Cyclin-dependent kinase 11B
E: Cyclin-dependent kinase 11B
F: Cyclin-dependent kinase 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,47418
Polymers219,5436
Non-polymers2,93112
Water00
1
A: Cyclin-dependent kinase 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0793
Polymers36,5901
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyclin-dependent kinase 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0793
Polymers36,5901
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cyclin-dependent kinase 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0793
Polymers36,5901
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cyclin-dependent kinase 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0793
Polymers36,5901
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cyclin-dependent kinase 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0793
Polymers36,5901
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cyclin-dependent kinase 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0793
Polymers36,5901
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.678, 146.678, 230.939
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Cyclin-dependent kinase 11B / Cell division cycle 2-like protein kinase 1 / CLK-1 / Cell division protein kinase 11B / ...Cell division cycle 2-like protein kinase 1 / CLK-1 / Cell division protein kinase 11B / Galactosyltransferase-associated protein kinase p58/GTA / PITSLRE serine/threonine-protein kinase CDC2L1 / p58 CLK-1


Mass: 36590.480 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK11B, CDC2L1, CDK11, PITSLREA, PK58 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21127, cyclin-dependent kinase
#2: Chemical
ChemComp-NK3 / OTS964


Mass: 392.514 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H24N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.75M NH4SO4, 0.1M Tris-HCl pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.65
ReflectionResolution: 2.6→127.03 Å / Num. obs: 86275 / % possible obs: 99.9 % / Redundancy: 8.58 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.117 / Χ2: 0.823 / Net I/σ(I): 15.27 / Num. measured all: 740270
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.768.6972.0551.0112029013956138310.3112.18499.1
2.76-2.958.7851.1991.9311512313104131040.6291.274100
2.95-3.188.4960.6073.9810388412228122280.8930.647100
3.18-3.498.3660.2678.829390711225112250.9810.285100
3.49-3.98.8760.13717.659022510165101650.9930.146100
3.9-4.58.4860.07928.7676098896889670.9970.085100
4.5-5.518.2260.06335.2362566760876060.9970.067100
5.51-7.788.7560.05241.8551605589558940.9980.055100
7.78-127.038.1630.03454.7926572325532550.9990.036100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.27 Å127.03 Å
Translation3.27 Å127.03 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
XDS20210322data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDS20210322data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IW8 homology model

2iw8


Resolution: 2.6→127.03 Å / Cross valid method: THROUGHOUT / σ(F): 248.55 / Phase error: 39.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2361 4313 5 %
Rwork0.2224 81873 -
obs0.2451 86184 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.93 Å2 / Biso mean: 73.768 Å2 / Biso min: 42.63 Å2
Refinement stepCycle: final / Resolution: 2.6→127.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13231 0 198 0 13429
Biso mean--70.91 --
Num. residues----1774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.640.33051990.30773761396087
2.64-2.690.30692140.30044074428895
2.69-2.740.31072180.29964109432795
2.74-2.80.31582180.29484101431995
2.8-2.860.28872150.29664135435095
2.86-2.920.30842130.30564083429695
2.92-30.30872170.29434108432595
3-3.080.33242140.30694098431295
3.08-3.170.32252170.29494092430995
3.17-3.270.3032150.2894116433195
3.27-3.390.25622160.28554118433495
3.39-3.520.28782170.27834098431595
3.52-3.680.27952170.27094104432195
3.68-3.880.25332150.26024109432495
3.88-4.120.24242160.24174102431895
4.12-4.440.24182190.22364138435795
4.44-4.890.22282150.21144124433995
4.89-5.590.22832180.2054106432495
5.59-7.050.23122180.21524137435595
7.05-127.030.2452200.22164160438095

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