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- PDB-5hex: Crystal Structure of Human Hexokinase 2 with cmpd 30, a 2-amino-6... -

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Basic information

Entry
Database: PDB / ID: 5hex
TitleCrystal Structure of Human Hexokinase 2 with cmpd 30, a 2-amino-6-benzenesulfonamide glucosamine
ComponentsHexokinase-2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / 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-604 / Hexokinase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.734 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 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 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

Downloads & links

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Assembly

Deposited unit
A: Hexokinase-2
B: Hexokinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,4026
Polymers206,2052
Non-polymers2,1974
Water1,49583
1
A: Hexokinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2013
Polymers103,1031
Non-polymers1,0992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hexokinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2013
Polymers103,1031
Non-polymers1,0992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.032, 154.893, 114.825
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 103102.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HK2 / Plasmid: pET28LIC.H6.TEV.huHK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52789, hexokinase
#2: Sugar
ChemComp-604 / 2-[(3-bromobenzene-1-carbonyl)amino]-6-{[(4-carboxy-5-methylfuran-2-yl)sulfonyl]amino}-2,6-dideoxy-alpha-D-glucopyranos e / 5-[[(2~{R},3~{S},4~{R},5~{R},6~{S})-5-[(3-bromophenyl)carbonylamino]-3,4,6-tris(oxidanyl)oxan-2-yl]methylsulfamoyl]-2-m ethyl-furan-3-carboxylic acid / 2-[(3-bromobenzene-1-carbonyl)amino]-6-{[(4-carboxy-5-methylfuran-2-yl)sulfonyl]amino}-2,6-dideoxy-alpha-D-glucose / 2-[(3-bromobenzene-1-carbonyl)amino]-6-{[(4-carboxy-5-methylfuran-2-yl)sulfonyl]amino}-2,6-dideoxy-D-glucose / 2-[(3-bromobenzene-1-carbonyl)amino]-6-{[(4-carboxy-5-methylfuran-2-yl)sulfonyl]amino}-2,6-dideoxy-glucose


Type: D-saccharide, alpha linking / Mass: 549.346 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H21BrN2O10S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 5
Details: protein conditions: 10mgs/mL, 50mM TRIS HCL, pH 7.5, 250mM NaCl, 2mM DTT, 2mM MgCl2. and 1mM cmpd30 Reservoir: 0.1M Na Citrate pH=5, 14% PEG 3350, 10 % ethylene glycol Cryo protectant 20% ...Details: protein conditions: 10mgs/mL, 50mM TRIS HCL, pH 7.5, 250mM NaCl, 2mM DTT, 2mM MgCl2. and 1mM cmpd30 Reservoir: 0.1M Na Citrate pH=5, 14% PEG 3350, 10 % ethylene glycol Cryo protectant 20% ethylene glycol in mother liquor
PH range: 5 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.73→114.12 Å / Num. obs: 59924 / % possible obs: 98.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 12.3
Reflection shellResolution: 2.73→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 2.734→114.12 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 2918 4.88 %
Rwork0.1899 --
obs0.193 59830 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.734→114.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13613 0 129 83 13825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913964
X-RAY DIFFRACTIONf_angle_d1.20518826
X-RAY DIFFRACTIONf_dihedral_angle_d13.9158376
X-RAY DIFFRACTIONf_chiral_restr0.062112
X-RAY DIFFRACTIONf_plane_restr0.0072461

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