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- PDB-7ezr: Indole-2-carboxylic acid derivatives as allosteric inhibitors of ... -

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Basic information

Entry
Database: PDB / ID: 7ezr
TitleIndole-2-carboxylic acid derivatives as allosteric inhibitors of fructose-1,6-bisphosphatase
ComponentsFructose-1,6-bisphosphatase 1
KeywordsHYDROLASE / fructose-1 / 6-bisphosphatase / indole-2-carboxylic acids
Function / homology
Function and homology information


cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / monosaccharide binding / negative regulation of glycolytic process / fructose 1,6-bisphosphate metabolic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / AMP binding / dephosphorylation / cellular response to cAMP / response to nutrient levels / gluconeogenesis / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain
Similarity search - Domain/homology
Chem-0H1 / 1,6-di-O-phosphono-beta-D-fructofuranose / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsWang, X.Y. / Zhou, J. / Xu, B.L.
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Discovery of Novel Indole Derivatives as Fructose-1,6-bisphosphatase Inhibitors and X-ray Cocrystal Structures Analysis.
Authors: Wang, X. / Zhao, R. / Ji, W. / Zhou, J. / Liu, Q. / Zhao, L. / Shen, Z. / Liu, S. / Xu, B.
History
DepositionJun 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)150,71612
Polymers147,5504
Non-polymers3,1668
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18720 Å2
ΔGint-87 kcal/mol
Surface area42120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.902, 142.591, 73.575
Angle α, β, γ (deg.)90.000, 108.657, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 (E. coli) / References: UniProt: P09467, fructose-bisphosphatase
#2: Chemical
ChemComp-0H1 / 5-ethyl-7-nitro-3-[3-oxidanylidene-3-(thiophen-2-ylsulfonylamino)propyl]-1H-indole-2-carboxylic acid


Mass: 451.473 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H17N3O7S2 / 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
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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
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: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.27→47.54 Å / Num. obs: 20178 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 66.69 Å2 / CC1/2: 0.995 / Net I/σ(I): 12.4
Reflection shellResolution: 3.27→3.53 Å / Num. unique obs: 20178 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FIE

2fie


Resolution: 3.27→40.84 Å / SU ML: 0.4571 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.1718
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2528 1025 5.09 %
Rwork0.2106 19114 -
obs0.2128 20139 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.91 Å2
Refinement stepCycle: LAST / Resolution: 3.27→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9790 0 200 0 9990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003910170
X-RAY DIFFRACTIONf_angle_d0.911213774
X-RAY DIFFRACTIONf_chiral_restr0.05081555
X-RAY DIFFRACTIONf_plane_restr0.0061745
X-RAY DIFFRACTIONf_dihedral_angle_d17.63631419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.27-3.440.34741530.26512688X-RAY DIFFRACTION99.09
3.44-3.660.32741410.25732746X-RAY DIFFRACTION99.93
3.66-3.940.27471510.23462722X-RAY DIFFRACTION100
3.94-4.340.27321530.20752727X-RAY DIFFRACTION100
4.34-4.970.20851410.1892726X-RAY DIFFRACTION99.9
4.97-6.250.26291260.20792761X-RAY DIFFRACTION99.97
6.25-40.840.19741600.17682744X-RAY DIFFRACTION98.94

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