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- PDB-5hg1: Crystal Structure of Human Hexokinase 2 with cmpd 1, a C-2-substi... -

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Basic information

Entry
Database: PDB / ID: 5hg1
TitleCrystal Structure of Human Hexokinase 2 with cmpd 1, a C-2-substituted glucosamine
ComponentsHexokinase-2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / metabolism / inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of mitochondrial membrane permeability / hexokinase activity / maintenance of protein location in mitochondrion / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / regulation of glucose import / establishment of protein localization to mitochondrion / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity ...negative regulation of mitochondrial membrane permeability / hexokinase activity / maintenance of protein location in mitochondrion / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / regulation of glucose import / establishment of protein localization to mitochondrion / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / glucose binding / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / apoptotic mitochondrial changes / intracellular glucose homeostasis / negative regulation of reactive oxygen species metabolic process / lactation / cellular response to leukemia inhibitory factor / sarcoplasmic reticulum / response to ischemia / glycolytic process / glucose metabolic process / positive regulation of angiogenesis / mitochondrial outer membrane / response to hypoxia / intracellular membrane-bounded organelle / centrosome / mitochondrion / ATP binding / membrane / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-62C / 6-O-phosphono-beta-D-glucopyranose / CITRATE ANION / Hexokinase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.76 Å
AuthorsCampobasso, N. / Zhao, B. / Smallwood, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Discovery of a Novel 2,6-Disubstituted Glucosamine Series of Potent and Selective Hexokinase 2 Inhibitors.
Authors: Lin, H. / Zeng, J. / Xie, R. / Schulz, M.J. / Tedesco, R. / Qu, J. / Erhard, K.F. / Mack, J.F. / Raha, K. / Rendina, A.R. / Szewczuk, L.M. / Kratz, P.M. / Jurewicz, A.J. / Cecconie, T. / ...Authors: Lin, H. / Zeng, J. / Xie, R. / Schulz, M.J. / Tedesco, R. / Qu, J. / Erhard, K.F. / Mack, J.F. / Raha, K. / Rendina, A.R. / Szewczuk, L.M. / Kratz, P.M. / Jurewicz, A.J. / Cecconie, T. / Martens, S. / McDevitt, P.J. / Martin, J.D. / Chen, S.B. / Jiang, Y. / Nickels, L. / Schwartz, B.J. / Smallwood, A. / Zhao, B. / Campobasso, N. / Qian, Y. / Briand, J. / Rominger, C.M. / Oleykowski, C. / Hardwicke, M.A. / Luengo, J.I.
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hexokinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1515
Polymers102,9451
Non-polymers1,2064
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-5 kcal/mol
Surface area36140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.120, 165.120, 126.478
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hexokinase-2 / / Hexokinase type II / HK II / Muscle form hexokinase


Mass: 102945.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52789, hexokinase
#2: Chemical ChemComp-62C / 2-deoxy-2-{[(2E)-3-(3,4-dichlorophenyl)prop-2-enoyl]amino}-alpha-D-glucopyranose


Mass: 378.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17Cl2NO6
#3: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.83 Å3/Da / Density % sol: 74.56 %
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: protein: 6.6 mgs/mL, 10mM Tris HCL, pH=8, 0.1 M NaCl, 1mM DTT, 20mM MgCl2 Well: 0.2 M Na Citrate pH 5.5, 14-24 % PEG3350, 20 % ethylene glycol
PH range: 5 - 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.76→126.48 Å / Num. obs: 51701 / % possible obs: 100 % / Redundancy: 11.2 % / Net I/σ(I): 18.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 2.76→71.499 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 2476 4.8 %
Rwork0.2177 --
obs0.22 51597 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.76→71.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6528 0 77 8 6613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086701
X-RAY DIFFRACTIONf_angle_d1.2349041
X-RAY DIFFRACTIONf_dihedral_angle_d10.8525455
X-RAY DIFFRACTIONf_chiral_restr0.0691043
X-RAY DIFFRACTIONf_plane_restr0.0091173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7554-2.80840.38491400.33382712X-RAY DIFFRACTION100
2.8084-2.86570.33851340.30962661X-RAY DIFFRACTION100
2.8657-2.92810.39081300.29222705X-RAY DIFFRACTION100
2.9281-2.99620.37191000.28952740X-RAY DIFFRACTION100
2.9962-3.07110.33181340.28752705X-RAY DIFFRACTION100
3.0711-3.15410.31741710.282681X-RAY DIFFRACTION100
3.1541-3.2470.3241590.28012685X-RAY DIFFRACTION100
3.247-3.35180.33341380.25812700X-RAY DIFFRACTION100
3.3518-3.47150.3071490.24082707X-RAY DIFFRACTION100
3.4715-3.61050.26351230.22692720X-RAY DIFFRACTION100
3.6105-3.77490.25041380.22032731X-RAY DIFFRACTION100
3.7749-3.97390.29311520.21292704X-RAY DIFFRACTION100
3.9739-4.22280.2691330.19362738X-RAY DIFFRACTION100
4.2228-4.54880.21591490.17632720X-RAY DIFFRACTION100
4.5488-5.00650.22811250.16992756X-RAY DIFFRACTION100
5.0065-5.73060.20681260.19672791X-RAY DIFFRACTION100
5.7306-7.21890.26031220.22392803X-RAY DIFFRACTION100
7.2189-71.52310.22791530.1912862X-RAY DIFFRACTION99

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