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- PDB-7nb3: Crystal structure of human choline alpha in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 7nb3
TitleCrystal structure of human choline alpha in complex with an inhibitor
ComponentsCholine kinase alpha
KeywordsTRANSFERASE / PHOSPHATIDYLCHOLINE / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-U6H / Choline kinase alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCasale, E. / Fasolini, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: Identification of unprecedented ATP-competitive choline kinase inhibitors.
Authors: Quartieri, F. / Nesi, M. / Avanzi, N.R. / Borghi, D. / Casale, E. / Corti, E. / Cucchi, U. / Donati, D. / Fasolini, M. / Felder, E.R. / Galvani, A. / Giorgini, M.L. / Lomolino, A. / ...Authors: Quartieri, F. / Nesi, M. / Avanzi, N.R. / Borghi, D. / Casale, E. / Corti, E. / Cucchi, U. / Donati, D. / Fasolini, M. / Felder, E.R. / Galvani, A. / Giorgini, M.L. / Lomolino, A. / Menichincheri, M. / Orrenius, C. / Perrera, C. / Re Depaolini, S. / Riccardi-Sirtori, F. / Salsi, E. / Isacchi, A. / Gnocchi, P.
History
DepositionJan 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Choline kinase alpha
BBB: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6749
Polymers90,0232
Non-polymers1,6517
Water5,098283
1
AAA: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9565
Polymers45,0121
Non-polymers9444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7184
Polymers45,0121
Non-polymers7063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.926, 120.199, 131.187
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: 45011.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GLY 74 IS AN EXPRESSION TAG / Source: (gene. exp.) Homo sapiens (human) / Gene: CHKA, CHK, CKI / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: P35790, choline kinase, ethanolamine kinase
#2: Chemical ChemComp-U6H / 4-(6-azanyl-2-pyridin-4-yl-purin-9-yl)-~{N}-(3-methoxyphenyl)cyclohexane-1-carboxamide


Mass: 443.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N7O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18-20% Peg-mme 5000, 0.1 M Magnesium Formate, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→47.3 Å / Num. obs: 60320 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8653 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CKQ

2ckq


Resolution: 2→41.128 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.175 / SU B: 4.612 / SU ML: 0.124 / Average fsc free: 0.8958 / Average fsc work: 0.9108 / Cross valid method: NONE / ESU R: 0.168 / ESU R Free: 0.157
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2342 3047 5.057 %
Rwork0.1893 57209 -
all0.192 --
obs-60256 99.45 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.519 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--2.442 Å2-0 Å2
3----1.582 Å2
Refinement stepCycle: LAST / Resolution: 2→41.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5749 0 113 283 6145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126055
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6558177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94921.424330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.998151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3831543
X-RAY DIFFRACTIONr_chiral_restr0.1060.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024585
X-RAY DIFFRACTIONr_nbd_refined0.2120.22715
X-RAY DIFFRACTIONr_nbtor_refined0.3220.24137
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2333
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.26
X-RAY DIFFRACTIONr_mcbond_it3.413.8632816
X-RAY DIFFRACTIONr_mcangle_it4.7545.7663518
X-RAY DIFFRACTIONr_scbond_it4.5984.1913239
X-RAY DIFFRACTIONr_scangle_it6.6526.1154656
X-RAY DIFFRACTIONr_lrange_it8.28950.8969311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.322180.2934177X-RAY DIFFRACTION99.7503
2.052-2.1080.272220.2624032X-RAY DIFFRACTION99.0915
2.108-2.1690.2952300.2373970X-RAY DIFFRACTION99.6205
2.169-2.2360.2542090.2173851X-RAY DIFFRACTION99.7788
2.236-2.3090.2531820.213776X-RAY DIFFRACTION99.7983
2.309-2.390.2891750.2123602X-RAY DIFFRACTION99.7623
2.39-2.480.2521830.23506X-RAY DIFFRACTION99.7836
2.48-2.5820.2481790.23358X-RAY DIFFRACTION99.159
2.582-2.6960.2611760.1983278X-RAY DIFFRACTION99.5963
2.696-2.8280.2631690.1963085X-RAY DIFFRACTION99.5107
2.828-2.9810.2491710.22938X-RAY DIFFRACTION99.488
2.981-3.1610.241310.1932820X-RAY DIFFRACTION99.6286
3.161-3.3790.2641460.2042610X-RAY DIFFRACTION98.7106
3.379-3.6490.2251580.1822454X-RAY DIFFRACTION99.7708
3.649-3.9970.1781150.1662289X-RAY DIFFRACTION99.5445
3.997-4.4680.1791170.1372063X-RAY DIFFRACTION99.3619
4.468-5.1570.201800.1381838X-RAY DIFFRACTION98.1576
5.157-6.310.238670.181606X-RAY DIFFRACTION99.7615
6.31-8.9010.243690.2071238X-RAY DIFFRACTION98.6415

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