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- PDB-5eqp: Crystal structure of choline kinase alpha-1 bound by 6-[(4-methyl... -

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Basic information

Entry
Database: PDB / ID: 5eqp
TitleCrystal structure of choline kinase alpha-1 bound by 6-[(4-methyl-1,4-diazepan-1-yl)methyl]quinoline (compound 37)
ComponentsCholine kinase alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / inhibitor / complex / drug target / 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 / phosphorylation / 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
6-[(4-methyl-1,4-diazepan-1-yl)methyl]quinoline / Choline kinase alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 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 13, 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 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / 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)94,2244
Polymers93,7132
Non-polymers5112
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-11 kcal/mol
Surface area32910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.495, 120.211, 130.285
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-5R9 / 6-[(4-methyl-1,4-diazepan-1-yl)methyl]quinoline


Mass: 255.358 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
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: Feb 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 37094 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.077 / Χ2: 1.066 / Net I/av σ(I): 20.506 / Net I/σ(I): 10 / Num. measured all: 198232
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.434.90.6936510.88199.5
2.43-2.535.20.58236480.96999.9
2.53-2.655.30.43736661.04999.9
2.65-2.795.30.30636691.09899.9
2.79-2.965.30.23436591.10399.8
2.96-3.195.30.15636651.10899.8
3.19-3.515.40.09537031.06899.8
3.51-4.025.60.05337490.966100
4.02-5.065.70.04137771.06699.9
5.06-505.40.04139071.31598.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
CNXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G15

3g15


Resolution: 2.35→50 Å / FOM work R set: 0.8137 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2638 1726 4.6 %
Rwork0.2266 32955 -
obs-34681 93.4 %
Displacement parametersBiso max: 116.07 Å2 / Biso mean: 49.4484 Å2 / Biso min: 16.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.081 Å20 Å20 Å2
2---0.134 Å20 Å2
3---0.215 Å2
Refinement stepCycle: final / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5831 0 89 0 5920
Biso mean--40.86 --
Num. residues----701
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4441.5
X-RAY DIFFRACTIONc_scbond_it2.1012
X-RAY DIFFRACTIONc_mcangle_it2.4542
X-RAY DIFFRACTIONc_scangle_it3.1932.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 34

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.35-2.370.4282350.3618858893
2.37-2.40.338420.347854896
2.4-2.420.3517480.3423872920
2.42-2.450.3183530.3126875928
2.45-2.480.3378400.2955874914
2.48-2.510.308470.3095876923
2.51-2.540.4049470.3402921968
2.54-2.570.4019540.3001897951
2.57-2.60.3112500.2813898948
2.6-2.640.2956590.2853924983
2.64-2.680.3483380.3032940978
2.68-2.720.3737420.2707943985
2.72-2.760.2909470.284948995
2.76-2.80.2322490.243938987
2.8-2.850.3543440.26919591003
2.85-2.90.346450.26399771022
2.9-2.960.3540.2713939993
2.96-3.020.2868560.2719641020
3.02-3.090.2919630.26139741037
3.09-3.160.2631560.26969691025
3.16-3.240.2786610.260210051066
3.24-3.330.3346490.245510111060
3.33-3.420.3144530.239810081061
3.42-3.530.2813340.236510311065
3.53-3.660.3004520.216410311083
3.66-3.810.2431560.208710171073
3.81-3.980.2579630.20110231086
3.98-4.190.1901650.187310161081
4.19-4.450.2124550.181910431098
4.45-4.790.2033520.176910491101
4.79-5.280.1903470.175710591106
5.28-6.040.2601520.228610731125
6.04-7.60.3118530.212610811134
7.6-500.2027650.175511081173
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 DIFFRACTION5AP29295_A_new.param

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