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- PDB-9vf9: GSTM1 in complex with bithionol -

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Basic information

Entry
Database: PDB / ID: 9vf9
TitleGSTM1 in complex with bithionol
ComponentsGlutathione S-transferase Mu 1
KeywordsTRANSFERASE / GST / inhibitor
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / glutathione transferase ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / glutathione metabolic process / enzyme binding / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
2,2'-sulfanediylbis(4,6-dichlorophenol) / Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSun, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81502629 China
CitationJournal: To Be Published
Title: Bithionol Targets GSTs to Increase Oxidative Stress and Enhance Doxorubicin Efficacy
Authors: Sun, Q.
History
DepositionJun 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase Mu 1
B: Glutathione S-transferase Mu 1
C: Glutathione S-transferase Mu 1
D: Glutathione S-transferase Mu 1
E: Glutathione S-transferase Mu 1
F: Glutathione S-transferase Mu 1
G: Glutathione S-transferase Mu 1
H: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,89518
Polymers205,9758
Non-polymers1,92010
Water4,035224
1
A: Glutathione S-transferase Mu 1
B: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3906
Polymers51,4942
Non-polymers8964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-17 kcal/mol
Surface area19440 Å2
MethodPISA
2
C: Glutathione S-transferase Mu 1
D: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9424
Polymers51,4942
Non-polymers4482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-18 kcal/mol
Surface area19470 Å2
MethodPISA
3
E: Glutathione S-transferase Mu 1
F: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6784
Polymers51,4942
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-19 kcal/mol
Surface area19510 Å2
MethodPISA
4
G: Glutathione S-transferase Mu 1
H: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8854
Polymers51,4942
Non-polymers3922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-29 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.209, 212.239, 91.645
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutathione S-transferase Mu 1 / GST HB subunit 4 / GST class-mu 1 / GSTM1-1 / GSTM1a-1a / GSTM1b-1b / GTH4


Mass: 25746.842 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTM1, GST1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09488, glutathione transferase
#2: Chemical
ChemComp-B1T / 2,2'-sulfanediylbis(4,6-dichlorophenol)


Mass: 356.052 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C12H6Cl4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Amino acids, 0.1 M MES pH 6.0 - 7.0, 40%-50% Mix1 (Mix1: 40% v/v PEG550*MME, 20% w/v PEG20000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.49→45.63 Å / Num. obs: 65334 / % possible obs: 98.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.116 / Net I/σ(I): 7.03
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 2895 / CC1/2: 0.402

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.63 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.907 / SU B: 36.225 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R: 1.527 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26664 3265 5 %RANDOM
Rwork0.23797 ---
obs0.23942 61656 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.386 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å2-0 Å2-3.48 Å2
2---0.97 Å20 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 2.5→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14496 0 107 224 14827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01214993
X-RAY DIFFRACTIONr_bond_other_d0.0010.01614165
X-RAY DIFFRACTIONr_angle_refined_deg11.86520221
X-RAY DIFFRACTIONr_angle_other_deg0.3731.77832788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35851736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.636580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.807102752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0530.22085
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023439
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_it1.8843.686968
X-RAY DIFFRACTIONr_mcbond_other1.8843.686968
X-RAY DIFFRACTIONr_mcangle_it3.2736.6078696
X-RAY DIFFRACTIONr_mcangle_other3.2736.6088697
X-RAY DIFFRACTIONr_scbond_it1.763.848025
X-RAY DIFFRACTIONr_scbond_other1.7593.848026
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0287.00911526
X-RAY DIFFRACTIONr_long_range_B_refined5.50435.1616998
X-RAY DIFFRACTIONr_long_range_B_other5.49635.0816975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 281 -
Rwork0.385 4388 -
obs--97.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.338-0.1472-0.29771.99770.63470.45960.0099-0.022-0.12840.1237-0.0036-0.19540.1454-0.0877-0.00630.0784-0.00410.00740.1816-0.0110.4403-16.3615.226-29.839
21.0354-0.0454-0.77781.79330.36630.7110.2227-0.01680.1107-0.0961-0.1716-0.0352-0.2104-0.0664-0.05110.0740.02010.0590.16070.00480.4395-19.42939.91-28.364
31.45390.18090.19720.7405-0.371.1468-0.0555-0.2626-0.0988-0.17890.05-0.01870.20210.0470.00550.05980.02040.01590.2067-0.01330.45564.55816.57417.583
41.97130.5918-0.26491.3702-0.25630.4105-0.0044-0.32120.3252-0.1459-0.01630.1771-0.04250.03350.02060.0295-0.0076-0.0250.1773-0.10610.5551.50141.13314.484
50.0613-0.25290.26575.3916-0.82081.6158-0.07090.04990.00370.62010.1359-0.39610.01570.0683-0.0650.3066-0.0292-0.0710.15540.00130.3583-6.50367.983-51.392
60.0288-0.3228-0.10745.09731.3950.4492-0.05250.01750.08720.92260.276-0.67940.2282-0.0554-0.22350.23180.0858-0.13890.26930.01270.4965-3.05592.279-48.493
70.5114-1.44360.04694.1548-0.0291.0630.20860.2181-0.1511-0.4479-0.60490.4067-0.08490.31280.39630.26960.0089-0.21350.19390.04810.345717.91168.682-6.842
80.9305-1.73130.5093.5795-0.86050.94810.17510.26460.080.0111-0.5323-0.0998-0.25460.17450.35730.4775-0.0494-0.13130.10160.06390.254216.54293.507-3.4
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 218
2X-RAY DIFFRACTION1A301 - 303
3X-RAY DIFFRACTION2B1 - 218
4X-RAY DIFFRACTION2B301
5X-RAY DIFFRACTION3C1 - 218
6X-RAY DIFFRACTION3C301 - 302
7X-RAY DIFFRACTION4D1 - 218
8X-RAY DIFFRACTION5E1 - 218
9X-RAY DIFFRACTION5E301 - 302
10X-RAY DIFFRACTION6F1 - 218
11X-RAY DIFFRACTION7G1 - 218
12X-RAY DIFFRACTION7G301
13X-RAY DIFFRACTION8H1 - 218
14X-RAY DIFFRACTION8H301

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