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- PDB-8s6i: Crystal structure of the human CDKL2 kinase domain with Compound 9 -

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Basic information

Entry
Database: PDB / ID: 8s6i
TitleCrystal structure of the human CDKL2 kinase domain with Compound 9
ComponentsCyclin-dependent kinase-like 2
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


sex differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / signal transduction / nucleoplasm / ATP binding ...sex differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / 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
: / Cyclin-dependent kinase-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsChen, X. / Ni, X. / Brooke, L. / Bullock, A.N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2.
Authors: Bashore, F.M. / Min, S.M. / Chen, X. / Howell, S. / Rinderle, C.H. / Morel, G. / Silvaroli, J.A. / Wells, C.I. / Bunnell, B.A. / Drewry, D.H. / Pabla, N.S. / Ultanir, S.K. / Bullock, A.N. / Axtman, A.D.
History
DepositionFeb 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0396
Polymers38,3901
Non-polymers6485
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-4 kcal/mol
Surface area15630 Å2
Unit cell
Length a, b, c (Å)58.093, 58.093, 104.261
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein Cyclin-dependent kinase-like 2 / Protein kinase p56 KKIAMRE / Serine/threonine-protein kinase KKIAMRE


Mass: 38390.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDKL2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92772, cyclin-dependent kinase
#2: Chemical ChemComp-A1H5G / ~{N}-[6-[3-[(2-methylpropylsulfonylamino)methyl]phenyl]-1~{H}-indazol-3-yl]cyclopropanecarboxamide


Mass: 426.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 119 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.09M Sodium fluoride, 0.09M Sodium bromide, 0.09M Sodium iodide; 0.1M Tris, 0.1M BICINE, pH8.5; 33% v/v Ethylene glycol; 16 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.72→52.13 Å / Num. obs: 41802 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 40.93 Å2 / CC1/2: 1 / Net I/σ(I): 22.7
Reflection shellResolution: 1.72→1.75 Å / Num. unique obs: 2106 / CC1/2: 0.51

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2.multiplexdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→50.31 Å / SU ML: 0.225 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.1495
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2219 2003 4.8 %
Rwork0.2046 39691 -
obs0.2055 41694 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.67 Å2
Refinement stepCycle: LAST / Resolution: 1.72→50.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 43 119 2618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522563
X-RAY DIFFRACTIONf_angle_d0.82823455
X-RAY DIFFRACTIONf_chiral_restr0.0505372
X-RAY DIFFRACTIONf_plane_restr0.008440
X-RAY DIFFRACTIONf_dihedral_angle_d13.9612340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.36421720.38642808X-RAY DIFFRACTION98.81
1.76-1.810.33141300.32532852X-RAY DIFFRACTION99.77
1.81-1.860.307950.27372858X-RAY DIFFRACTION99.73
1.86-1.920.25661360.26542821X-RAY DIFFRACTION100
1.93-1.990.29871350.2692874X-RAY DIFFRACTION99.93
1.99-2.070.27791450.25062839X-RAY DIFFRACTION99.83
2.07-2.170.24441700.21562799X-RAY DIFFRACTION99.97
2.17-2.280.25241540.262813X-RAY DIFFRACTION99.93
2.28-2.430.27931200.25212873X-RAY DIFFRACTION99.97
2.43-2.610.26491380.24112826X-RAY DIFFRACTION99.93
2.61-2.880.26311720.24622820X-RAY DIFFRACTION100
2.88-3.290.25091540.232822X-RAY DIFFRACTION100
3.29-4.150.19011380.17642870X-RAY DIFFRACTION100
4.15-50.310.1751440.1572816X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 11.2928873674 Å / Origin y: 20.4458542699 Å / Origin z: -16.4345448857 Å
111213212223313233
T0.29799928501 Å2-0.00950000332594 Å2-0.012964482299 Å2-0.306282207612 Å20.0278454097381 Å2--0.347235445663 Å2
L1.64779679705 °2-0.184572200763 °20.0498672463746 °2-0.133945193912 °20.182319757949 °2--1.68493774617 °2
S0.0658446759721 Å °-0.149595644614 Å °-0.0470431501057 Å °-0.0293893243534 Å °-0.0224118339322 Å °0.0222129034173 Å °0.127249744234 Å °-0.126660894763 Å °-0.000617950797814 Å °
Refinement TLS groupSelection details: all

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