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- PDB-3s41: Glucokinase in complex with activator and glucose -

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Basic information

Entry
Database: PDB / ID: 3s41
TitleGlucokinase in complex with activator and glucose
ComponentsGlucokinase
KeywordsTRANSFERASE / DIABETES MELLITUS / DISEASE MUTATION / GLYCOLYSIS
Function / homology
Function and homology information


Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / mannokinase activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucose catabolic process / glucokinase activity / glucose 6-phosphate metabolic process ...Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / mannokinase activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucose catabolic process / glucokinase activity / glucose 6-phosphate metabolic process / NADP metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / D-glucose binding / cellular response to leptin stimulus / canonical glycolysis / calcium ion import / Glycolysis / regulation of glycolytic process / intracellular glucose homeostasis / Regulation of gene expression in beta cells / positive regulation of glycogen biosynthetic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to glucose / regulation of insulin secretion / glycolytic process / positive regulation of insulin secretion / cellular response to insulin stimulus / glucose metabolic process / glucose homeostasis / mitochondrion / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / Chem-S41 / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.18 Å
AuthorsLiu, S.
CitationJournal: MEDCHEMCOMM / Year: 2011
Title: Designing glucokinase activators with reduced hypoglycemia risk: discovery of N,N-dimethyl-5-(2-methyl-6-((5-methylpyrazin-2-yl)-carbamoyl)benzofuran-4-yloxy)pyrimidine-2-carboxamide as a ...Title: Designing glucokinase activators with reduced hypoglycemia risk: discovery of N,N-dimethyl-5-(2-methyl-6-((5-methylpyrazin-2-yl)-carbamoyl)benzofuran-4-yloxy)pyrimidine-2-carboxamide as a clinical candidate for the treatment of type 2 diabetes mellitus
Authors: Pfefferkorn, J.A. / Guzman-Perez, A. / Oates, P.J. / Litchfield, J. / Aspnes, G. / Basak, A. / Benbow, J. / Berliner, M.A. / Bian, J. / Choi, C. / Freeman-Cook, K. / Corbett, J.W. / Didiuk, ...Authors: Pfefferkorn, J.A. / Guzman-Perez, A. / Oates, P.J. / Litchfield, J. / Aspnes, G. / Basak, A. / Benbow, J. / Berliner, M.A. / Bian, J. / Choi, C. / Freeman-Cook, K. / Corbett, J.W. / Didiuk, M. / Dunetz, J.R. / Filipski, K.J. / Hungerford, W.M. / Jones, C.S. / Karki, K. / Ling, A. / Li, J.-C. / Patel, L. / Perreault, C. / Risley, H. / Saenz, J. / Song, W. / Tu, M. / Aiello, R. / Atkinson, K. / Barucci, N. / Beebe, D. / Bourassa, P. / Bourbounais, F. / Brodeur, A.M. / Burbey, R. / Chen, J. / D'Aquila, T. / Derksen, D.R. / Haddish-Berhane, N. / Huang, C. / Landro, J. / Lapworth, A.L. / MacDougall, M. / Perregaux, D. / Pettersen, J. / Robertson, A. / Tan, B. / Treadway, J.L. / Liu, S. / Qiu, X. / Knafels, J. / Ammirati, M. / Song, X. / DaSilva-Jardine, P. / Liras, S. / Sweet, L. / Rolph, T.P.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5754
Polymers52,9391
Non-polymers6363
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.010, 82.200, 86.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucokinase / Hexokinase type IV / HK IV / Hexokinase-4 / HK4 / Hexokinase-D


Mass: 52939.133 Da / Num. of mol.: 1 / Fragment: sequence database residues 12-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCK / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35557, glucokinase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-S41 / N,N-dimethyl-5-({2-methyl-6-[(5-methylpyrazin-2-yl)carbamoyl]-1-benzofuran-4-yl}oxy)pyrimidine-2-carboxamide


Mass: 432.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→82.2 Å / Num. obs: 22198 / % possible obs: 87.1 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 28.91 Å2 / Rmerge(I) obs: 0.115

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Processing

SoftwareName: BUSTER / Version: 2.9.3 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3FGU

3fgu


Resolution: 2.18→52.9 Å / Cor.coef. Fo:Fc: 0.9274 / Cor.coef. Fo:Fc free: 0.8777 / SU R Cruickshank DPI: 0.316 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.342 / SU Rfree Blow DPI: 0.234 / SU Rfree Cruickshank DPI: 0.231
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 1105 4.99 %RANDOM
Rwork0.1898 ---
obs0.1926 22127 86.85 %-
Displacement parametersBiso mean: 28.46 Å2
Baniso -1Baniso -2Baniso -3
1-3.2357 Å20 Å20 Å2
2---4.5448 Å20 Å2
3---1.3091 Å2
Refine analyzeLuzzati coordinate error obs: 0.266 Å
Refinement stepCycle: LAST / Resolution: 2.18→52.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 45 181 3732
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013651HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.174918HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1361SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes539HARMONIC5
X-RAY DIFFRACTIONt_it3651HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion19.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion460SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4397SEMIHARMONIC4
LS refinement shellResolution: 2.18→2.29 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2414 66 5.33 %
Rwork0.1992 1173 -
all0.2015 1239 -
obs--86.85 %

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