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- PDB-7a06: Structure of human CKa1 in complex with compound o -

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Basic information

Entry
Database: PDB / ID: 7a06
TitleStructure of human CKa1 in complex with compound o
ComponentsCholine kinase alpha
KeywordsTRANSFERASE / Choline kinase / drugs / cancer / anti proliferative effect / half molecules
Function / homology
Function and homology information


ethanolamine kinase / choline kinase / ethanolamine kinase activity / Synthesis of PE / choline kinase activity / CDP-choline pathway / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / Synthesis of PE / choline kinase activity / CDP-choline pathway / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity / lipid transport / Synthesis of PC / cellular response to glucose starvation / lipid droplet / lipid metabolic process / protein tyrosine kinase activity / protein homodimerization activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Choline/ethanolamine kinase / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-QTH / Choline kinase alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSerran-Aguilera, L. / Mariotto, E. / Rubbini, G. / Castro Navas, F.C. / Marco, C. / Carrasco-Jimenez, M.P. / Ballarotto, M. / Macchiarulo, A. / Hurtado-Guerrero, R. / Viola, G. / Lopez-Cara, L.C.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Synthesis, biological evaluation, in silico modeling and crystallization of novel small monocationic molecules with potent antiproliferative activity by dual mechanism.
Authors: Serran-Aguilera, L. / Mariotto, E. / Rubbini, G. / Castro Navas, F.F. / Marco, C. / Carrasco-Jimenez, M.P. / Ballarotto, M. / Macchiarulo, A. / Hurtado-Guerrero, R. / Viola, G. / Lopez-Cara, L.C.
History
DepositionAug 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,39216
Polymers44,9541
Non-polymers1,43815
Water6,431357
1
A: Choline kinase alpha
hetero molecules

A: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,78432
Polymers89,9092
Non-polymers2,87530
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area6010 Å2
ΔGint44 kcal/mol
Surface area34890 Å2
Unit cell
Length a, b, c (Å)61.374, 61.374, 221.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Choline kinase alpha / CK / CHETK-alpha / Ethanolamine kinase / EK


Mass: 44954.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHKA, CHK, CKI / Production host: Escherichia coli (E. coli)
References: UniProt: P35790, choline kinase, ethanolamine kinase
#2: Chemical ChemComp-QTH / 1-[(4-phenylphenyl)methyl]-4-pyrrolidin-1-yl-pyridine


Mass: 315.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 magensium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→200 Å / Num. obs: 40416 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.6
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.653 / Num. unique obs: 5751

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G15

3g15


Resolution: 1.8→61.37 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.751 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22994 1146 2.8 %RANDOM
Rwork0.18867 ---
obs0.18983 39176 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.462 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.8→61.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 100 357 3398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193198
X-RAY DIFFRACTIONr_bond_other_d0.0030.023051
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9964297
X-RAY DIFFRACTIONr_angle_other_deg0.8843.0047044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.375377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43523.396159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68815576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.091525
X-RAY DIFFRACTIONr_chiral_restr0.0850.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02782
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2311.5851449
X-RAY DIFFRACTIONr_mcbond_other1.2291.5831448
X-RAY DIFFRACTIONr_mcangle_it2.0312.3651817
X-RAY DIFFRACTIONr_mcangle_other2.0312.3671818
X-RAY DIFFRACTIONr_scbond_it1.7911.9131749
X-RAY DIFFRACTIONr_scbond_other1.7911.9131749
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9362.7382471
X-RAY DIFFRACTIONr_long_range_B_refined5.98314.373944
X-RAY DIFFRACTIONr_long_range_B_other5.98314.3323938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 68 -
Rwork0.248 2860 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: -16.969 Å / Origin y: 17.3383 Å / Origin z: 6.6197 Å
111213212223313233
T0.0572 Å20.0001 Å2-0.0126 Å2-0.0549 Å2-0.0213 Å2--0.0117 Å2
L0.0876 °2-0.1014 °20.0471 °2-0.2533 °2-0.1743 °2--0.4116 °2
S-0.0164 Å °0.0352 Å °-0.0075 Å °0.0597 Å °0.0243 Å °-0.0228 Å °0.0013 Å °-0.0109 Å °-0.0079 Å °

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