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- PDB-3nc9: X-ray structure of ketohexokinase complexed with an indazole compound -

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Basic information

Entry
Database: PDB / ID: 3nc9
TitleX-ray structure of ketohexokinase complexed with an indazole compound
ComponentsKetohexokinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ketohexokinase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Essential fructosuria / ketohexokinase / ketohexokinase activity / fructose binding / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion ...Essential fructosuria / ketohexokinase / ketohexokinase activity / fructose binding / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ketohexokinase / : / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TR3 / Ketohexokinase / Isoform A of Ketohexokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAbad, M.C. / Gibbs, A.C. / Spurlino, J.C.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Electron density guided fragment-based lead discovery of ketohexokinase inhibitors.
Authors: Gibbs, A.C. / Abad, M.C. / Zhang, X. / Tounge, B.A. / Lewandowski, F.A. / Struble, G.T. / Sun, W. / Sui, Z. / Kuo, L.C.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2017Group: Structure summary
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Ketohexokinase
B: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0786
Polymers68,1532
Non-polymers9254
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-50 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.696, 85.692, 136.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ketohexokinase / Hepatic fructokinase


Mass: 34076.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Plasmid: pET28s / Production host: Escherichia coli (E. coli)
References: UniProt: P50053-2, UniProt: P50053*PLUS, ketohexokinase
#2: Chemical ChemComp-TR3 / N-[3-(methylsulfanyl)-1-phenyl-1H-indazol-6-yl]piperidine-4-carboxamide


Mass: 366.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N4OS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.56 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 17% PEG8k, 0.1M Na-Citrate, 0.2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2009 / Details: mirrors
RadiationMonochromator: double crystal mono, Si(111) from accel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→44.9 Å / Num. all: 38770 / Num. obs: 38469 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.64 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.64 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3856

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Processing

Software
NameVersionClassification
JDirectordata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3NBV

3nbv


Resolution: 2.4→36.314 Å / SU ML: 0.43 / Isotropic thermal model: anisotropic / σ(F): 0.04 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2852 1917 5.19 %
Rwork0.2374 --
obs0.2399 36922 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.121 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.9783 Å20 Å20 Å2
2--6.222 Å2-0 Å2
3---2.7563 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4555 0 62 39 4656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094706
X-RAY DIFFRACTIONf_angle_d1.1646370
X-RAY DIFFRACTIONf_dihedral_angle_d16.2931736
X-RAY DIFFRACTIONf_chiral_restr0.073700
X-RAY DIFFRACTIONf_plane_restr0.006839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.35371380.29742427X-RAY DIFFRACTION94
2.46-2.52650.32421220.27562434X-RAY DIFFRACTION93
2.5265-2.60090.33451360.27392393X-RAY DIFFRACTION93
2.6009-2.68480.34031360.28312420X-RAY DIFFRACTION94
2.6848-2.78070.32341320.27792443X-RAY DIFFRACTION94
2.7807-2.8920.34531410.27362437X-RAY DIFFRACTION94
2.892-3.02360.38031340.28622458X-RAY DIFFRACTION95
3.0236-3.18290.37351470.28992526X-RAY DIFFRACTION96
3.1829-3.38220.32451330.26542525X-RAY DIFFRACTION98
3.3822-3.64310.29641400.22952585X-RAY DIFFRACTION98
3.6431-4.00930.23461430.20712555X-RAY DIFFRACTION98
4.0093-4.58840.20711400.18382636X-RAY DIFFRACTION98
4.5884-5.77720.22411410.1872639X-RAY DIFFRACTION99
5.7772-36.31840.2711340.22152527X-RAY DIFFRACTION90

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