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- PDB-7nb1: Crystal structure of human choline alpha in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 7nb1
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 / 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 / cytoplasm / cytosol
Similarity search - Function
Choline/ethanolamine kinase / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-U6T / Choline kinase alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)91,6757
Polymers90,0232
Non-polymers1,6525
Water2,558142
1
AAA: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9574
Polymers45,0121
Non-polymers9453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7183
Polymers45,0121
Non-polymers7072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.855, 122.003, 132.121
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-U6T / 4-(6-aminopurin-9-yl)-~{N}-[4-(trifluoromethylsulfonyl)phenyl]cyclohexane-1-carboxamide


Mass: 468.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19F3N6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
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: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→47.4 Å / Num. obs: 40989 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5891 / % possible all: 100

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Processing

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

2ckq


Resolution: 2.3→44.857 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.184 / SU B: 7.444 / SU ML: 0.174 / Average fsc free: 0.8945 / Average fsc work: 0.9141 / Cross valid method: FREE R-VALUE / ESU R: 0.292 / ESU R Free: 0.229
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2486 2094 5.117 %
Rwork0.1946 38831 -
all0.197 --
obs-40925 99.937 %
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: 55.247 Å2
Baniso -1Baniso -2Baniso -3
1--0.612 Å20 Å20 Å2
2--3.361 Å2-0 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5788 0 109 142 6039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126055
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.6568175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02821.722331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9921541
X-RAY DIFFRACTIONr_chiral_restr0.1120.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024565
X-RAY DIFFRACTIONr_nbd_refined0.2190.22523
X-RAY DIFFRACTIONr_nbtor_refined0.3170.24114
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2236
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.214
X-RAY DIFFRACTIONr_mcbond_it4.6225.3182812
X-RAY DIFFRACTIONr_mcangle_it6.5847.9493508
X-RAY DIFFRACTIONr_scbond_it6.1855.7313243
X-RAY DIFFRACTIONr_scangle_it8.8478.3844667
X-RAY DIFFRACTIONr_lrange_it10.91768.5748959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3161570.2872816X-RAY DIFFRACTION99.8656
2.36-2.4240.3361530.2712759X-RAY DIFFRACTION100
2.424-2.4950.3161590.272648X-RAY DIFFRACTION99.9644
2.495-2.5710.3551220.2562628X-RAY DIFFRACTION99.9636
2.571-2.6560.3441160.2522566X-RAY DIFFRACTION100
2.656-2.7490.3431480.2212416X-RAY DIFFRACTION100
2.749-2.8520.2681390.2142365X-RAY DIFFRACTION100
2.852-2.9690.2671320.2162272X-RAY DIFFRACTION100
2.969-3.1010.2771370.2192183X-RAY DIFFRACTION99.9569
3.101-3.2520.2861310.2132094X-RAY DIFFRACTION99.9551
3.252-3.4270.2771070.2261992X-RAY DIFFRACTION99.9524
3.427-3.6350.243880.2011912X-RAY DIFFRACTION99.9001
3.635-3.8850.219810.1831801X-RAY DIFFRACTION100
3.885-4.1960.189610.1531714X-RAY DIFFRACTION99.9437
4.196-4.5950.189880.1461545X-RAY DIFFRACTION99.9388
4.595-5.1360.168740.1371418X-RAY DIFFRACTION100
5.136-5.9280.212540.1651268X-RAY DIFFRACTION100
5.928-7.2520.268690.1951074X-RAY DIFFRACTION99.9126

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