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- PDB-4ctn: Glucopyranosylidene-spiro-iminothiazolidinone, a New Bicyclic Rin... -

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Basic information

Entry
Database: PDB / ID: 4ctn
TitleGlucopyranosylidene-spiro-iminothiazolidinone, a New Bicyclic Ring System: Synthesis, Derivatization, and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetic and Crystallographic Methods
ComponentsGLYCOGEN PHOSPHORYLASE, MUSCLE FORM
KeywordsTRANSFERASE / TYPE 2 DIABETES / INHIBITOR / STRUCTURE-BASED DRUG DESIGN
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-M8P / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAlexacou, K.M. / Papakonstantinou, M. / Leonidas, D.D. / Zographos, S.E. / Chrysina, E.D.
Citation
Journal: Bioorg.Med.Chem. / Year: 2014
Title: Glucopyranosylidene-Spiro-Iminothiazolidinone, a New Bicyclic Ring System: Synthesis, Derivatization, and Evaluation for Inhibition of Glycogen Phosphorylase by Enzyme Kinetic and Crystallographic Methods.
Authors: Czifrak, K. / Deak, S. / Pahi, A. / Kover, K.E. / Docsa, T. / Gergely, P. / Alexacou, K.M. / Papakonstantinou, M. / Leonidas, D.D. / Zographos, S.E. / Chrysina, E.D. / Somsak, L.
#1: Journal: Protein Sci. / Year: 1998
Title: The Structure of a Glycogen Phosphorylase Glucopyranose Spirohydantoin Complex at 1.8 A Resolution and 100 K: The Role of the Water Structure and its Contribution to Binding.
Authors: Gregoriou, M. / Noble, M.E. / Watson, K.A. / Garman, E.F. / Krulle, T.M. / De La Fuente, C. / Fleet, G.W. / Oikonomakos, N.G. / Johnson, L.N.
History
DepositionMar 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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 / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3205
Polymers97,4221
Non-polymers8984
Water2,936163
1
A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules

A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,64110
Polymers194,8452
Non-polymers1,7968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5700 Å2
ΔGint-14.8 kcal/mol
Surface area56450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.760, 127.760, 116.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GLYCOGEN PHOSPHORYLASE, MUSCLE FORM / MYOPHOSPHORYLASE


Mass: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase

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Non-polymers , 5 types, 167 molecules

#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-M8P / N-[(2Z,5R,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-4-oxo-6-oxa-1-thia-3-azaspiro[4.5]dec-2-ylidene]naphthalene-2-carboxamide


Mass: 418.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N2O7S
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.44 Å3/Da / Density % sol: 49.64 % / Description: NONE
Crystal growpH: 6.8
Details: 25MG/ML ENZYME, 1MM SPERMINE, 10MM BES, 3MM DTT, 0.1MM EDTA, PH 6.7, AT 16OC.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.04498
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 16, 2007 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04498 Å / Relative weight: 1
ReflectionResolution: 2.1→35.7 Å / Num. obs: 55833 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→32.03 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PYD

2pyd


Resolution: 2.1→32.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.39 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21837 2836 5.1 %RANDOM
Rwork0.18119 ---
obs0.18305 52967 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.192 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6562 0 56 163 6781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196766
X-RAY DIFFRACTIONr_bond_other_d0.0010.026463
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.969161
X-RAY DIFFRACTIONr_angle_other_deg0.7223.00114798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55223.536345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.562151169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5011559
X-RAY DIFFRACTIONr_chiral_restr0.060.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021644
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_it1.6623.9143225
X-RAY DIFFRACTIONr_mcbond_other1.6623.9133224
X-RAY DIFFRACTIONr_mcangle_it2.6635.864026
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0794.2693541
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 199 -
Rwork0.239 3860 -
obs--99.31 %

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