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- PDB-3ie3: Structural basis for the binding of the anti-cancer compound 6-(7... -

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Basic information

Entry
Database: PDB / ID: 3ie3
TitleStructural basis for the binding of the anti-cancer compound 6-(7-Nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX) to human glutathione S-transferases
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / detoxification / multidrug resistance / cancer treatment / Phosphoprotein / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process ...nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / negative regulation of leukocyte proliferation / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / Paracetamol ADME / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / negative regulation of MAPK cascade / Detoxification of Reactive Oxygen Species / glutathione transferase / negative regulation of acute inflammatory response / glutathione transferase activity / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / glutathione metabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / xenobiotic metabolic process / response to reactive oxygen species / regulation of ERK1 and ERK2 cascade / negative regulation of MAP kinase activity / positive regulation of superoxide anion generation / central nervous system development / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / secretory granule lumen / cellular response to lipopolysaccharide / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Chem-N11 / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsFederici, L. / Lo Sterzo, C. / Di Matteo, A. / Scaloni, F. / Federici, G. / Caccuri, A.M.
CitationJournal: Cancer Res. / Year: 2009
Title: Structural basis for the binding of the anticancer compound 6-(7-nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol to human glutathione s-transferases
Authors: Federici, L. / Lo Sterzo, C. / Pezzola, S. / Di Matteo, A. / Scaloni, F. / Federici, G. / Caccuri, A.M.
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Non-polymer description / Structure summary
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 1, 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: Glutathione S-transferase P
B: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0098
Polymers46,4092
Non-polymers1,6006
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-19 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.869, 89.535, 68.916
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

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Components

#1: Protein Glutathione S-transferase P / GST class-pi / GSTP1-1


Mass: 23204.490 Da / Num. of mol.: 2 / Mutation: I104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P09211, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-N11 / 6-[(7-nitro-2,1,3-benzoxadiazol-4-yl)sulfanyl]hexan-1-ol / 6-(7-Nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol


Mass: 297.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15N3O4S
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8M AMMONIUM SULFATE, 100MM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 1, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→29.21 Å / Num. all: 42435 / Num. obs: 42435 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 17.4
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 8.05 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
FFTmodel building
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 6GSS

6gss


Resolution: 1.8→29.21 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.305 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.13 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20938 2132 5 %RANDOM
Rwork0.17887 ---
all0.18042 42435 --
obs0.18042 40294 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.588 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å2-0.12 Å2
2---1.24 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 104 473 3840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223453
X-RAY DIFFRACTIONr_angle_refined_deg1.3732.0144690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5385425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.16124.765149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95915561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7261516
X-RAY DIFFRACTIONr_chiral_restr0.1530.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022620
X-RAY DIFFRACTIONr_nbd_refined0.1770.21697
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22364
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0850.2393
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.219
X-RAY DIFFRACTIONr_mcbond_it0.3171.52168
X-RAY DIFFRACTIONr_mcangle_it0.51723349
X-RAY DIFFRACTIONr_scbond_it0.72631505
X-RAY DIFFRACTIONr_scangle_it1.1164.51337
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 132 -
Rwork0.212 2763 -
obs--91.04 %

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