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- PDB-7nb2: Crystal structure of human choline alpha in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 7nb2
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-U6E / Choline kinase alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site

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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)91,5709
Polymers90,0232
Non-polymers1,5477
Water1,24369
1
AAA: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9045
Polymers45,0121
Non-polymers8934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6664
Polymers45,0121
Non-polymers6543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.593, 120.926, 130.456
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 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-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
#3: Chemical ChemComp-U6E / 4-(6-azanyl-2-chloranyl-purin-9-yl)-~{N}-(4-methyl-1,3-thiazol-2-yl)cyclohexane-1-carboxamide


Mass: 391.878 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18ClN7OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
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: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.4→55.59 Å / Num. obs: 35130 / % possible obs: 99.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 19
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.689 / Num. unique obs: 3644 / % possible all: 99.9

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Processing

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

2ckq


Resolution: 2.4→51.196 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.179 / SU B: 9.759 / SU ML: 0.218 / Average fsc free: 0.8712 / Average fsc work: 0.8921 / Cross valid method: NONE / ESU R: 0.38 / ESU R Free: 0.254
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2477 1718 4.899 %
Rwork0.2017 33353 -
all0.204 --
obs-35071 99.571 %
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: 62.682 Å2
Baniso -1Baniso -2Baniso -3
1--1.157 Å20 Å20 Å2
2--5.936 Å2-0 Å2
3----4.779 Å2
Refinement stepCycle: LAST / Resolution: 2.4→51.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5702 0 99 69 5870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125956
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.6518045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52521.739322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.302151019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8651539
X-RAY DIFFRACTIONr_chiral_restr0.1060.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024507
X-RAY DIFFRACTIONr_nbd_refined0.2230.22567
X-RAY DIFFRACTIONr_nbtor_refined0.3160.24050
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2202
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.21
X-RAY DIFFRACTIONr_mcbond_it4.8956.252791
X-RAY DIFFRACTIONr_mcangle_it7.139.3493480
X-RAY DIFFRACTIONr_scbond_it6.2286.453165
X-RAY DIFFRACTIONr_scangle_it8.5839.5134565
X-RAY DIFFRACTIONr_lrange_it10.78480.6748889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.361420.2932420X-RAY DIFFRACTION99.8441
2.462-2.530.3931080.2852398X-RAY DIFFRACTION99.9203
2.53-2.6030.3181120.2722292X-RAY DIFFRACTION100
2.603-2.6830.3141240.2562252X-RAY DIFFRACTION100
2.683-2.7710.3231140.2352202X-RAY DIFFRACTION99.9137
2.771-2.8680.361120.2272084X-RAY DIFFRACTION99.8182
2.868-2.9770.239920.232037X-RAY DIFFRACTION99.6723
2.977-3.0980.281230.2121961X-RAY DIFFRACTION99.6176
3.098-3.2360.294870.2151877X-RAY DIFFRACTION99.4934
3.236-3.3940.266860.1961788X-RAY DIFFRACTION99.0486
3.394-3.5770.243780.2021744X-RAY DIFFRACTION99.6173
3.577-3.7940.273640.2031654X-RAY DIFFRACTION99.5365
3.794-4.0550.228860.1941533X-RAY DIFFRACTION99.3861
4.055-4.380.218820.1741429X-RAY DIFFRACTION99.6702
4.38-4.7980.178730.1591329X-RAY DIFFRACTION100
4.798-5.3630.215720.1661202X-RAY DIFFRACTION99.8433
5.363-6.1910.226600.211092X-RAY DIFFRACTION99.4819
6.191-7.5780.246490.205918X-RAY DIFFRACTION99.7936
7.578-10.6990.193400.154731X-RAY DIFFRACTION98.8462

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