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- PDB-4cg9: Human choline kinase a1 in complex with compound 12 -

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Basic information

Entry
Database: PDB / ID: 4cg9
TitleHuman choline kinase a1 in complex with compound 12
ComponentsCHOLINE KINASE ALPHA
KeywordsTRANSFERASE / CANCER / DRUG TARGET / BISCATIONIC COMPOUNDS
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 / 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-GQG / Choline kinase alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 1.2Mar 12, 2014Group: Source and taxonomy
Revision 1.3Dec 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

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Assembly

Deposited unit
A: CHOLINE KINASE ALPHA
A: N,N-dimethyl-1-[(4-phenylphenyl)methyl]pyridin-1-ium-4-amine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2442
Polymers44,9541
Non-polymers2891
Water1,44180
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.080, 61.080, 220.560
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-GQG / N,N-dimethyl-1-[(4-phenylphenyl)methyl]pyridin-1-ium-4-amine


Mass: 289.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.29 Å3/Da / Density % sol: 46.24 % / Description: NONE

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Data collection

DiffractionMean temperature: 73 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.83→61.08 Å / Num. obs: 37763 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.3
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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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: 1.83→61.08 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.737 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25618 1883 5 %RANDOM
Rwork0.22852 ---
obs0.22991 35792 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.035 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.83→61.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 22 80 3035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023044
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9764102
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1315355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68123.355152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5515554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0191523
X-RAY DIFFRACTIONr_chiral_restr0.0980.2421
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: 1.834→1.882 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 120 -
Rwork0.282 2319 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -16.8922 Å / Origin y: 17.1806 Å / Origin z: 6.5413 Å
111213212223313233
T0.0363 Å2-0.0113 Å2-0.0045 Å2-0.014 Å2-0.001 Å2--0.0492 Å2
L0.0834 °2-0.0829 °20.0459 °2-0.1523 °2-0.1628 °2--0.2593 °2
S-0.0188 Å °0.011 Å °-0.0278 Å °0.017 Å °0.0046 Å °-0.0048 Å °-0.0064 Å °-0.0223 Å °0.0142 Å °

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