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- PDB-8jub: Crystal structure of glutaminase C in complex with compound 27 -

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Basic information

Entry
Database: PDB / ID: 8jub
TitleCrystal structure of glutaminase C in complex with compound 27
ComponentsGlutaminase kidney isoform, mitochondrial
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / Complex / ANTITUMOR PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes / chemical synaptic transmission / protein homotetramerization / mitochondrial matrix / synapse / mitochondrion / cytosol
Similarity search - Function
Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Beta-lactamase/transpeptidase-like / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Chem-V4I / Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsWang, X. / Hanyu, S. / Tingting, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)CIFMS, No. 2021-I2M-1-028 United Kingdom
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Targeting the Subpocket Enables the Discovery of Thiadiazole-Pyridazine Derivatives as Glutaminase C Inhibitors.
Authors: Sun, H. / Du, T. / Yang, M. / Liu, X. / Xue, X. / Chen, K. / Lang, X. / Chen, X. / Wang, B. / Wang, X.
History
DepositionJun 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaminase kidney isoform, mitochondrial
B: Glutaminase kidney isoform, mitochondrial
C: Glutaminase kidney isoform, mitochondrial
D: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,9746
Polymers235,1234
Non-polymers8512
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-40 kcal/mol
Surface area59450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.479, 138.710, 178.425
Angle α, β, γ (deg.)90.00, 93.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutaminase kidney isoform, mitochondrial / GLS / K-glutaminase / L-glutamine amidohydrolase


Mass: 58780.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94925, glutaminase
#2: Chemical ChemComp-V4I / 3-[2-oxidanylidene-2-[[5-[[(3R)-1-pyridazin-3-ylpyrrolidin-3-yl]amino]-1,3,4-thiadiazol-2-yl]amino]ethyl]benzoic acid


Mass: 425.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N7O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% Polyethylene glycol 3350, 0.2 M magnesium chloride, 0.08 M 2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonicacid pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.01→89.24 Å / Num. obs: 145402 / % possible obs: 91.18 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07234 / Rpim(I) all: 0.03351 / Rrim(I) all: 0.07993 / Net I/σ(I): 15.72
Reflection shellResolution: 2.01→2.082 Å / Rmerge(I) obs: 0.6913 / Num. unique obs: 11575 / CC1/2: 0.708 / Rpim(I) all: 0.3733 / Rrim(I) all: 0.789

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.01→89.24 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.393 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21713 7239 5 %RANDOM
Rwork0.19226 ---
obs0.19346 138154 91.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.943 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20.29 Å2
2---0.59 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 2.01→89.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12421 0 60 387 12868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212756
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.64717201
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29451574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.134560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.139102232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.21891
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029500
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.0623.4836335
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3075.1927896
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5064.0256421
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.56454.45718937
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 526 -
Rwork0.267 11048 -
obs--98.16 %

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