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- PDB-7cvn: The N-arylsulfonyl-indole-2-carboxamide-based inhibitors against ... -

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Basic information

Entry
Database: PDB / ID: 7cvn
TitleThe N-arylsulfonyl-indole-2-carboxamide-based inhibitors against fructose-1,6-bisphosphatase
ComponentsFructose-1,6-bisphosphatase 1
KeywordsHYDROLASE / Fructose-1 / 6-bisphosphatase / N-arylsulfonyl-indole-2-carboxamide
Function / homology
Function and homology information


cellular response to raffinose / cellular hypotonic salinity response / fructose-bisphosphatase / cellular response to phorbol 13-acetate 12-myristate / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / Gluconeogenesis / fructose metabolic process ...cellular response to raffinose / cellular hypotonic salinity response / fructose-bisphosphatase / cellular response to phorbol 13-acetate 12-myristate / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / Gluconeogenesis / fructose metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / negative regulation of glycolytic process / regulation of gluconeogenesis / cellular hyperosmotic salinity response / AMP binding / cellular response to cAMP / gluconeogenesis / response to nutrient levels / negative regulation of cell growth / cellular response to xenobiotic stimulus / cellular response to insulin stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / Chem-GJO / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWang, X. / Zhou, J. / Xu, B.
CitationJournal: Chinese journal of medicinal chemistry / Year: 2020
Title: Design,synthesis,biological evaluation and binding mode analysis of 7-nitro-indole-N-acylarylsulfonamide-based fructose-1,6-bisphosphatase inhibitors
Authors: Bie, J. / Wang, X. / Liu, S. / Zhou, J. / Liu, Q. / Shen, Z. / Xu, B.
History
DepositionAug 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,94412
Polymers147,5504
Non-polymers3,3948
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18610 Å2
ΔGint-90 kcal/mol
Surface area43520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.570, 83.000, 278.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Fructose-1,6-bisphosphatase 1 / FBPase 1 / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase 1 / Liver FBPase


Mass: 36887.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, FBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09467, fructose-bisphosphatase
#2: Chemical
ChemComp-GJO / 4-(3-acetamidophenyl)-N-(4-methoxyphenyl)sulfonyl-7-nitro-1H-indole-2-carboxamide


Mass: 508.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H20N4O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium acetate, 0.1M HEPES, 20% PEG 3350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97778 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 2.75→92.71 Å / Num. obs: 41781 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 17.85 Å2 / CC1/2: 0.971 / Net I/σ(I): 8.1
Reflection shellResolution: 2.75→2.86 Å / Num. unique obs: 49738 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FIE

2fie


Resolution: 2.75→21.52 Å / SU ML: 0.2577 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2338 2069 4.98 %
Rwork0.1633 39507 -
obs0.1669 41576 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.22 Å2
Refinement stepCycle: LAST / Resolution: 2.75→21.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9768 0 224 327 10319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007810176
X-RAY DIFFRACTIONf_angle_d0.980213783
X-RAY DIFFRACTIONf_chiral_restr0.05261546
X-RAY DIFFRACTIONf_plane_restr0.00521745
X-RAY DIFFRACTIONf_dihedral_angle_d16.48261444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.810.27151320.18922614X-RAY DIFFRACTION99.93
2.81-2.880.30611390.17852551X-RAY DIFFRACTION100
2.88-2.960.27151260.18542639X-RAY DIFFRACTION100
2.96-3.050.24681230.18232592X-RAY DIFFRACTION100
3.05-3.150.25921360.17942585X-RAY DIFFRACTION99.96
3.15-3.260.2351480.17122592X-RAY DIFFRACTION100
3.26-3.390.2621300.17632625X-RAY DIFFRACTION99.96
3.39-3.540.23891600.17082594X-RAY DIFFRACTION99.96
3.54-3.730.25381370.15792618X-RAY DIFFRACTION100
3.73-3.960.23081590.15052616X-RAY DIFFRACTION99.89
3.96-4.260.20071370.14112622X-RAY DIFFRACTION100
4.26-4.690.17131120.12582664X-RAY DIFFRACTION100
4.69-5.360.20041450.14112668X-RAY DIFFRACTION99.96
5.36-6.720.22871250.18152725X-RAY DIFFRACTION99.96
6.72-21.520.21521600.17572802X-RAY DIFFRACTION99.73

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