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- PDB-5ftg: Human choline kinase a1 in complex with compound 1-[[4-[2-[4-[[4-... -

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Basic information

Entry
Database: PDB / ID: 5ftg
TitleHuman choline kinase a1 in complex with compound 1-[[4-[2-[4-[[4-(dimethylamino)pyridin-1- yl]methyl]phenoxy]ethoxy]phenyl]methyl]-N,N- dimethyl-pyridin-4-amine (compound 10a)
ComponentsCHOLINE KINASE ALPHA
KeywordsTRANSFERASE / BISCATIONIC INHIBITOR / DOCKING STUDIES
Function / homology
Function and homology information


ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / 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 / phosphorylation / protein homodimerization activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Choline/ethanolamine kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NBR / Choline kinase alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSchiaffino-Ortega, S. / Baglioni, E. / Mariotto, E. / Bortolozzi, R. / Serran-Aguilera, L. / Rios-Marco, P. / Carrasco-Jimenez, M.P. / Gallo, M.A. / Hurtado-Guerrero, R. / Marco, C. ...Schiaffino-Ortega, S. / Baglioni, E. / Mariotto, E. / Bortolozzi, R. / Serran-Aguilera, L. / Rios-Marco, P. / Carrasco-Jimenez, M.P. / Gallo, M.A. / Hurtado-Guerrero, R. / Marco, C. / Basso, G. / Viola, G. / Entrena, A. / Lopez-Cara, L.C.
CitationJournal: Sci.Rep. / Year: 2016
Title: Design, Synthesis, Crystallization and Biological Evaluation of New Symmetrical Biscationic Compounds as Selective Inhibitors of Human Choline Kinase Alpha1 (Chokalpha1)
Authors: Schiaffino-Ortega, S. / Baglioni, E. / Mariotto, E. / Bortolozzi, R. / Serran-Aguilera, L. / Rios-Marco, P. / Carrasco-Jimenez, M.P. / Gallo, M.A. / Hurtado-Guerrero, R. / Marco, C. / Basso, ...Authors: Schiaffino-Ortega, S. / Baglioni, E. / Mariotto, E. / Bortolozzi, R. / Serran-Aguilera, L. / Rios-Marco, P. / Carrasco-Jimenez, M.P. / Gallo, M.A. / Hurtado-Guerrero, R. / Marco, C. / Basso, G. / Viola, G. / Entrena, A. / Lopez-Cara, L.C.
History
DepositionJan 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Structure summary
Revision 2.0Oct 23, 2019Group: Data collection / Non-polymer description / Other / Category: chem_comp / pdbx_database_status
Item: _chem_comp.formula / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHOLINE KINASE ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,56912
Polymers44,4641
Non-polymers1,10511
Water5,368298
1
A: CHOLINE KINASE ALPHA
hetero molecules

A: CHOLINE KINASE ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,13824
Polymers88,9282
Non-polymers2,21122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area6660 Å2
ΔGint52.8 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.650, 60.650, 220.404
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: 44463.902 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 80-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMALC2X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P35790, choline kinase, ethanolamine kinase
#2: Chemical ChemComp-NBR / 1-[[4-[2-[4-[[4-(dimethylamino)pyridin-1-yl]methyl]phenoxy]ethoxy]phenyl]methyl]-N,N-dimethyl-pyridin-4-amine


Mass: 484.632 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H36N4O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.03 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1.0507
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0507 Å / Relative weight: 1
ReflectionResolution: 1.45→58 Å / Num. obs: 74167 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 23.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.8
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 14 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G15

3g15


Resolution: 1.45→58.48 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.931 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2041 2.8 %RANDOM
Rwork0.197 ---
obs0.17367 74167 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.966 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.45→58.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 0 76 298 3310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193118
X-RAY DIFFRACTIONr_bond_other_d0.0020.022965
X-RAY DIFFRACTIONr_angle_refined_deg2.2311.9854182
X-RAY DIFFRACTIONr_angle_other_deg1.0213.0026831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76323.355152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.17515556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3111523
X-RAY DIFFRACTIONr_chiral_restr0.1350.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213457
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
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_it1.5971.3391436
X-RAY DIFFRACTIONr_mcbond_other1.591.3371435
X-RAY DIFFRACTIONr_mcangle_it2.4012.0031799
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2171.7631682
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 141 -
Rwork0.215 5193 -
obs--98.81 %
Refinement TLS params.Method: refined / Origin x: -16.5643 Å / Origin y: 17.1402 Å / Origin z: 6.5336 Å
111213212223313233
T0.0247 Å2-0.0084 Å20.0011 Å2-0.0284 Å2-0.0052 Å2--0.0012 Å2
L0.0136 °2-0.0195 °20.0323 °2-0.1053 °2-0.0548 °2--0.1647 °2
S-0.0059 Å °0.0126 Å °-0.0011 Å °0.0219 Å °0.0004 Å °-0.0049 Å °-0.0012 Å °-0.0048 Å °0.0055 Å °

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