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- PDB-4cga: Human choline kinase a1 in complex with compound 5 -

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Basic information

Entry
Database: PDB / ID: 4cga
TitleHuman choline kinase a1 in complex with compound 5
ComponentsCHOLINE KINASE ALPHA
KeywordsTRANSFERASE / CANCER / DRUG TARGET / BISCATIONIC COMPOUNDS
Function / homology
Function and homology information


ethanolamine kinase / choline kinase / Synthesis of PE / ethanolamine kinase activity / choline kinase activity / CDP-choline pathway / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / Synthesis of PE / ethanolamine kinase activity / 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 / 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-QLW / Choline kinase alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRubio-Ruiz, B. / Figuerola-Conchas, A. / Ramos-Torrecillas, J. / Capitan-Canadas, F. / Rios-Marco, P. / Carrasco, M.P. / Gallo, M.A. / Espinosa, A. / Marco, C. / Concepcion, C. ...Rubio-Ruiz, B. / Figuerola-Conchas, A. / Ramos-Torrecillas, J. / Capitan-Canadas, F. / Rios-Marco, P. / Carrasco, M.P. / Gallo, M.A. / Espinosa, A. / Marco, C. / Concepcion, C. / Entrena-Guadix, A. / Hurtado-Guerrero, R. / Conejo-Garcia, A.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Discovery of a New Binding Site on Human Choline Kinase A1: Design, Synthesis, Crystallographic Studies and Biological Evaluation of Asymmetrical Bispyridinium Derivatives
Authors: Rubio-Ruiz, B. / Figuerola-Conchas, A. / Ramos-Torrecillas, J. / Capitan-Canadas, F. / Rios-Marco, P. / Carrasco, M.P. / Gallo, M.A. / Espinosa, A. / Marco, C. / Concepcion, C. / Entrena- ...Authors: Rubio-Ruiz, B. / Figuerola-Conchas, A. / Ramos-Torrecillas, J. / Capitan-Canadas, F. / Rios-Marco, P. / Carrasco, M.P. / Gallo, M.A. / Espinosa, A. / Marco, C. / Concepcion, C. / Entrena-Guadix, A. / Hurtado-Guerrero, R. / Conejo-Garcia, A.
History
DepositionNov 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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
A: N,N-dimethyl-1-[[4-(2-phenylethyl)phenyl]methyl]pyridin-1-ium-4-amine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2722
Polymers44,9541
Non-polymers3171
Water5,423301
1
A: CHOLINE KINASE ALPHA
hetero molecules

A: CHOLINE KINASE ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5444
Polymers89,9092
Non-polymers6352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area2420 Å2
ΔGint-12.8 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.512, 61.512, 220.597
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 / CHOLINE KINASE A1


Mass: 44954.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 75-457
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-QLW / N,N-dimethyl-1-[[4-(2-phenylethyl)phenyl]methyl]pyridin-1-ium-4-amine


Mass: 317.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.02 % / Description: NONE

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Data collection

DiffractionMean temperature: 73 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.872
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 1.74→20 Å / Num. obs: 44468 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.4
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.7 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G15

3g15


Resolution: 1.74→220.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.145 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25783 1136 2.6 %RANDOM
Rwork0.21083 ---
obs0.21203 43236 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.74→220.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 24 301 3266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023046
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9764103
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.455354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60523.355152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31315552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0091523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212330
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.739→1.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 86 -
Rwork0.321 2619 -
obs--90.47 %
Refinement TLS params.Method: refined / Origin x: -16.9942 Å / Origin y: 17.432 Å / Origin z: 6.4352 Å
111213212223313233
T0.0444 Å2-0.0006 Å2-0.0072 Å2-0.0248 Å2-0.0156 Å2--0.0189 Å2
L0.0803 °2-0.0611 °20.0404 °2-0.1652 °2-0.1487 °2--0.2266 °2
S-0.008 Å °0.0354 Å °-0.0162 Å °0.0409 Å °0.0033 Å °-0.0167 Å °0.0044 Å °-0.0151 Å °0.0046 Å °

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