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- PDB-5afv: Pharmacophore-based virtual screening to discover new active comp... -

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Basic information

Entry
Database: PDB / ID: 5afv
TitlePharmacophore-based virtual screening to discover new active compounds for human choline kinase alpha1.
ComponentsCHOLINE KINASE ALPHA
KeywordsTRANSFERASE / VIRTUAL SCREENING / PHARMACOPHORE
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
1-benzyl-4-(benzylamino)-1H-1,2,4-triazol-4-ium / Choline kinase alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSerran-Aguilera, L. / Nuti, R. / Lopez-Cara, L.C. / Gallo Mezo, M.A. / Macchiarulo, A. / Entrena, A. / Hurtado-Guerrero, R.
CitationJournal: Mol Inform / Year: 2015
Title: Pharmacophore-Based Virtual Screening to Discover New Active Compounds for Human Choline Kinase Alpha1
Authors: Serran-Aguilera, L. / Nuti, R. / Lopez-Cara, L.C. / Gallo Mezo, M.A. / Macchiarulo, A. / Entrena, A. / Hurtado-Guerrero, R.
History
DepositionJan 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHOLINE KINASE ALPHA
B: CHOLINE KINASE ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,09611
Polymers88,9282
Non-polymers1,1689
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint5.9 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.129, 120.180, 132.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2633, 0.8559, 0.4451), (0.8563, -0.4198, 0.3008), (0.4443, 0.3019, -0.843)
Vector: 3.296, 12.53, -32.87)

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Components

#1: Protein CHOLINE KINASE ALPHA / CK / CHETK-ALPHA / ETHANOLAMINE KINASE / EK


Mass: 44463.902 Da / Num. of mol.: 2 / Fragment: RESIDUES 80-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMALC2X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P35790, choline kinase, ethanolamine kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-JH5 / 1-benzyl-4-(benzylamino)-1H-1,2,4-triazol-4-ium


Mass: 265.333 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H17N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.51 Å3/Da / Density % sol: 51.01 % / Description: NONE
Crystal growpH: 8.5 / Details: PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1.0507
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0507 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 43397 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 23.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.8
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 14 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G15

3g15


Resolution: 2.25→132.39 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.906 / SU B: 17.413 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26745 1236 2.9 %RANDOM
Rwork0.22419 ---
obs0.22548 41895 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.689 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20 Å2
2--0.87 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.25→132.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 84 269 6235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196161
X-RAY DIFFRACTIONr_bond_other_d0.0050.025843
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9848282
X-RAY DIFFRACTIONr_angle_other_deg1.1143.00213461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89723.355307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.039151113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5721547
X-RAY DIFFRACTIONr_chiral_restr0.0890.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216837
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021512
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3213.0982845
X-RAY DIFFRACTIONr_mcbond_other2.3223.0982844
X-RAY DIFFRACTIONr_mcangle_it3.6614.6313555
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7273.4923316
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 83 -
Rwork0.36 3010 -
obs--98.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04550.1377-0.09030.455-0.20981.00080.02930.0158-0.00970.0312-0.0046-0.0446-0.0529-0.0893-0.02470.14220.04550.01240.14690.01870.008712.3841-6.9254-4.592
20.4399-0.52070.00130.6789-0.20050.732-0.1108-0.07210.00740.08950.10620.00020.0674-0.02070.00470.10810.0101-0.02170.12370.01290.0419-1.706224.4744-25.6624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 457
2X-RAY DIFFRACTION2B80 - 457

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