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- PDB-5eqe: Crystal structure of choline kinase alpha-1 bound by [4-[(4-methy... -

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Basic information

Entry
Database: PDB / ID: 5eqe
TitleCrystal structure of choline kinase alpha-1 bound by [4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]methanamine (compound 11)
ComponentsCholine kinase alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-5R8 / Choline kinase alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsZhou, T. / Zhu, X. / Dalgarno, D.C.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Novel Small Molecule Inhibitors of Choline Kinase Identified by Fragment-Based Drug Discovery.
Authors: Zech, S.G. / Kohlmann, A. / Zhou, T. / Li, F. / Squillace, R.M. / Parillon, L.E. / Greenfield, M.T. / Miller, D.P. / Qi, J. / Thomas, R.M. / Wang, Y. / Xu, Y. / Miret, J.J. / Shakespeare, W. ...Authors: Zech, S.G. / Kohlmann, A. / Zhou, T. / Li, F. / Squillace, R.M. / Parillon, L.E. / Greenfield, M.T. / Miller, D.P. / Qi, J. / Thomas, R.M. / Wang, Y. / Xu, Y. / Miret, J.J. / Shakespeare, W.C. / Zhu, X. / Dalgarno, D.C.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Structure summary
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline kinase alpha
B: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1804
Polymers93,7132
Non-polymers4672
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.671, 120.878, 131.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46856.477 Da / Num. of mol.: 2 / Fragment: UNP residues 75-457
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-5R8 / [4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]methanamine


Mass: 233.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H23N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium formate, 8-12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35538 / % possible obs: 98.7 % / Redundancy: 3 % / Net I/σ(I): 19.5

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Processing

Software
NameVersionClassification
CNSrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
CNXphasing
RefinementResolution: 2.4→50 Å / FOM work R set: 0.8176 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2626 1652 4.7 %
Rwork0.2249 31697 -
obs-33349 94.1 %
Displacement parametersBiso max: 98.26 Å2 / Biso mean: 39.5985 Å2 / Biso min: 7.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.066 Å20 Å20 Å2
2---0.113 Å20 Å2
3---0.047 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5799 0 149 0 5948
Biso mean--38.74 --
Num. residues----697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4451.5
X-RAY DIFFRACTIONc_scbond_it2.0522
X-RAY DIFFRACTIONc_mcangle_it2.4472
X-RAY DIFFRACTIONc_scangle_it3.1022.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 33

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.420.2867440.2974874918
2.42-2.450.3407470.2893846893
2.45-2.480.3688490.3059902951
2.48-2.510.3271470.3067888935
2.51-2.540.3509500.2844908958
2.54-2.570.3299470.2809887934
2.57-2.60.2887410.261901942
2.6-2.630.345510.2634906957
2.63-2.670.3092530.2577919972
2.67-2.710.2372440.2488906950
2.71-2.750.2838530.27179651018
2.75-2.790.3465450.275948993
2.79-2.840.3551660.28649401006
2.84-2.880.3887320.2809965997
2.88-2.940.3283390.26919671006
2.94-2.990.344460.2533950996
2.99-3.050.2793410.25669901031
3.05-3.120.305620.23799851047
3.12-3.190.3194560.26519591015
3.19-3.270.3872560.25410041060
3.27-3.360.1958410.21899671008
3.36-3.460.2228650.22259921057
3.46-3.570.2555440.24299991043
3.57-3.70.2361540.207710011055
3.7-3.850.2893450.22639941039
3.85-4.020.2704660.2059991065
4.02-4.240.2167550.187610141069
4.24-4.50.1919620.17569881050
4.5-4.850.2353440.17110241068
4.85-5.340.2439420.18510251067
5.34-6.110.2067610.196710171078
6.11-7.690.2244600.1910231083
7.69-500.189440.201110441088
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5AP27736_B.param

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