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- PDB-2y5l: orally active aminopyridines as inhibitors of tetrameric fructose... -

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Basic information

Entry
Database: PDB / ID: 2y5l
Titleorally active aminopyridines as inhibitors of tetrameric fructose 1,6- bisphosphatase
ComponentsFRUCTOSE-1,6-BISPHOSPHATASE 1Fructose 1,6-bisphosphatase
KeywordsHYDROLASE
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 / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process ...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 / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process / fructose metabolic process / Gluconeogenesis / monosaccharide binding / negative regulation of glycolytic 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 / metal ion binding / nucleus / cytosol / cytoplasm
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 / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...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 / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-RO8 / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
Authorsruf, a. / hebeisen, p. / haap, w. / kuhn, b. / mohr, p. / wessel, h.p. / zutter, u. / kirchner, s. / benz, j. / joseph, c. ...ruf, a. / hebeisen, p. / haap, w. / kuhn, b. / mohr, p. / wessel, h.p. / zutter, u. / kirchner, s. / benz, j. / joseph, c. / alvarez-sanchez, r. / gubler, m. / schott, b. / benardeau, a. / tozzo, e. / kitas, e.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Orally Active Aminopyridines as Inhibitors of Tetrameric Fructose-1,6-Bisphosphatase.
Authors: Hebeisen, P. / Haap, W. / Kuhn, B. / Mohr, P. / Wessel, H.P. / Zutter, U. / Kirchner, S. / Ruf, A. / Benz, J. / Joseph, C. / Alvarez-Sanchez, R. / Gubler, M. / Schott, B. / Benardeau, A. / Tozzo, E. / Kitas, E.
History
DepositionJan 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_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_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: FRUCTOSE-1,6-BISPHOSPHATASE 1
B: FRUCTOSE-1,6-BISPHOSPHATASE 1
C: FRUCTOSE-1,6-BISPHOSPHATASE 1
D: FRUCTOSE-1,6-BISPHOSPHATASE 1
E: FRUCTOSE-1,6-BISPHOSPHATASE 1
F: FRUCTOSE-1,6-BISPHOSPHATASE 1
G: FRUCTOSE-1,6-BISPHOSPHATASE 1
H: FRUCTOSE-1,6-BISPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,04916
Polymers294,8758
Non-polymers3,1738
Water9,620534
1
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)149,0248
Polymers147,4384
Non-polymers1,5874
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15780 Å2
ΔGint-82.7 kcal/mol
Surface area44740 Å2
MethodPISA
2
E: FRUCTOSE-1,6-BISPHOSPHATASE 1
F: FRUCTOSE-1,6-BISPHOSPHATASE 1
G: FRUCTOSE-1,6-BISPHOSPHATASE 1
H: FRUCTOSE-1,6-BISPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,0248
Polymers147,4384
Non-polymers1,5874
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16690 Å2
ΔGint-82.8 kcal/mol
Surface area44450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.791, 285.084, 83.687
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 1000
2115B1 - 1000
3115C1 - 1000
4115D1 - 1000
5115E1 - 1000
6115F1 - 1000
7115G1 - 1000
8115H1 - 1000

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Components

#1: Protein
FRUCTOSE-1,6-BISPHOSPHATASE 1 / Fructose 1,6-bisphosphatase / FBPASE 1 / D-FRUCTOSE-1 / 6-BISPHOSPHATE 1-PHOSPHOHYDROLASE 1


Mass: 36859.418 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P09467, fructose-bisphosphatase
#2: Chemical
ChemComp-RO8 / N-{[(2Z)-5-bromo-1,3-thiazol-2(3H)-ylidene]carbamoyl}-3-chlorobenzenesulfonamide / RO5062408


Mass: 396.668 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H7BrClN3O3S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.68 Å3/Da / Density % sol: 54.11 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 11, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→99 Å / Num. obs: 155315 / % possible obs: 85.2 % / Observed criterion σ(I): -10 / Redundancy: 3.86 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.9
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.03 / % possible all: 7.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0093refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VT5

2vt5


Resolution: 2.2→142.86 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.197 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25375 7800 5 %RANDOM
Rwork0.20497 ---
obs0.20745 147515 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.454 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å20 Å20.22 Å2
2---1.26 Å20 Å2
3----2.55 Å2
Refinement stepCycle: LAST / Resolution: 2.2→142.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19440 0 160 534 20134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02219985
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.99927001
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87252524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07724.264774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.681153561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.31215102
X-RAY DIFFRACTIONr_chiral_restr0.0850.23062
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114774
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1268medium positional0.270.5
2B1268medium positional0.260.5
3C1268medium positional0.430.5
4D1268medium positional0.260.5
5E1268medium positional0.230.5
6F1268medium positional0.250.5
7G1268medium positional0.410.5
8H1268medium positional0.260.5
1A1172loose positional0.65
2B1172loose positional0.75
3C1172loose positional0.775
4D1172loose positional0.675
5E1172loose positional0.575
6F1172loose positional0.655
7G1172loose positional0.745
8H1172loose positional0.685
1A1268medium thermal5.042
2B1268medium thermal6.42
3C1268medium thermal6.732
4D1268medium thermal9.592
5E1268medium thermal10.562
6F1268medium thermal10.932
7G1268medium thermal6.122
8H1268medium thermal6.312
1A1172loose thermal6.4410
2B1172loose thermal7.2710
3C1172loose thermal810
4D1172loose thermal9.810
5E1172loose thermal10.510
6F1172loose thermal11.5510
7G1172loose thermal7.410
8H1172loose thermal7.0610
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 554 -
Rwork0.319 10745 -
obs--98.87 %

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