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

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Basic information

Entry
Database: PDB / ID: 7ezp
TitleIndole-2-carboxylic acid derivatives as allosteric inhibitors of fructose-1,6-bisphosphatase
ComponentsFructose-1,6-bisphosphatase 1
KeywordsHYDROLASE / fructose-1 / 6-bisphosphatase / indole dicarboxylic acid derivatives
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
Chem-0GI / 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: 2.8 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)150,24712
Polymers147,5504
Non-polymers2,6988
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18430 Å2
ΔGint-99 kcal/mol
Surface area42820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.100, 143.000, 73.600
Angle α, β, γ (deg.)90.000, 107.740, 90.000
Int Tables number4
Space group name H-MP1211
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: 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
#3: Chemical
ChemComp-0GI / 3-(3-hydroxy-3-oxopropyl)-5-(2-methylpropyl)-7-nitro-1H-indole-2-carboxylic acid


Mass: 334.324 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H18N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
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: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.8→71.5 Å / Num. obs: 32570 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.785 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.145 / Rrim(I) all: 0.205 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1 / % possible all: 99.7

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.8-2.9550.7892375647230.4740.4310.9034.4
8.85-71.54.80.084512310660.9820.0450.09619.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FIE

2fie


Resolution: 2.8→70.2 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.876 / SU B: 18.273 / SU ML: 0.351 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 1644 5.1 %RANDOM
Rwork0.2102 ---
obs0.2125 30821 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.71 Å2 / Biso mean: 35.488 Å2 / Biso min: 8.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0.04 Å2
2--0.1 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.8→70.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9765 0 176 149 10090
Biso mean--40.94 28.83 -
Num. residues----1279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310117
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179802
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.66813696
X-RAY DIFFRACTIONr_angle_other_deg1.5391.59722650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62751269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01222.545440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.907151771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2961552
X-RAY DIFFRACTIONr_chiral_restr0.0710.21316
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022085
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.321 112 -
Rwork0.283 2263 -
obs--99.04 %

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