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- PDB-3nc4: The binding of beta-D-glucopyranosyl-thiosemicarbazone derivative... -

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Basic information

Entry
Database: PDB / ID: 3nc4
TitleThe binding of beta-D-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: a new class of inhibitors
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Glycogenolysis / type 2 diabetes / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-26O / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.07 Å
AuthorsAlexacou, K.-M.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: The binding of beta-D-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: a new class of inhibitors
Authors: Alexacou, K.M. / Tenchiu Deleanu, A.C. / Chrysina, E.D. / Charavgi, M.D. / Kostas, I.D. / Zographos, S.E. / Oikonomakos, N.G. / Leonidas, D.D.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_distant_solvent_atoms ...diffrn_source / pdbx_distant_solvent_atoms / software / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name / _software.version
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 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
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1473
Polymers97,4321
Non-polymers7152
Water5,080282
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,2946
Polymers194,8642
Non-polymers1,4304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4720 Å2
ΔGint-27 kcal/mol
Surface area56000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.517, 128.517, 115.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 97432.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / Strain: Rabbit / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-26O / N-({(2E)-2-[(2-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucopyranosylamine / 2-hydroxybenzaldehyde-4-(beta-D-glucopyranosyl) thiosemicarbazone / N-({(2E)-2-[(2-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucosylamine / N-({(2E)-2-[(2-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-D-glucosylamine / N-({(2E)-2-[(2-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-glucosylamine


Type: D-saccharide / Mass: 357.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: Crystals grown from 20 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA, 3 mM DTT. Crystals were soaked with 20mM inhibitor in 20% DMSO for 21 hrs 10 mins, pH 6. ...Details: Crystals grown from 20 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA, 3 mM DTT. Crystals were soaked with 20mM inhibitor in 20% DMSO for 21 hrs 10 mins, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.815 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2009
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2.07→30 Å / Num. all: 48018 / Num. obs: 48018 / % possible obs: 80.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.59
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.72 / % possible all: 83.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2PRJ

2prj


Resolution: 2.07→27.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.109 / SU ML: 0.113 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21972 2431 5.1 %RANDOM
Rwork0.17973 ---
obs0.18176 45659 80.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.638 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.07→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 48 282 6934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226815
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.969228
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5275809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99223.534348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.267151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5541559
X-RAY DIFFRACTIONr_chiral_restr0.0830.2998
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025231
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.23026
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24619
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2375
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6511.54165
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11626524
X-RAY DIFFRACTIONr_scbond_it1.6133034
X-RAY DIFFRACTIONr_scangle_it2.5434.52704
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.119 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 187 -
Rwork0.217 3320 -
obs--81.37 %

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