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- PDB-9s48: Human SIRT2 in Complex with RW-80 -

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Basic information

Entry
Database: PDB / ID: 9s48
TitleHuman SIRT2 in Complex with RW-80
ComponentsNAD-dependent protein deacetylase sirtuin-2
KeywordsHYDROLASE / Inhibitior / Lysine deacetylase / NAD+-dependant enzyme / Epigenetics
Function / homology
Function and homology information


cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / negative regulation of striated muscle tissue development / negative regulation of satellite cell differentiation / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of attachment of spindle microtubules to kinetochore / positive regulation of meiotic nuclear division / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / negative regulation of striated muscle tissue development / negative regulation of satellite cell differentiation / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of attachment of spindle microtubules to kinetochore / positive regulation of meiotic nuclear division / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / peptidyl-lysine deacetylation / tubulin deacetylation / lateral loop / NLRP3 inflammasome complex assembly / negative regulation of NLRP3 inflammasome complex assembly / mitotic nuclear membrane reassembly / tubulin deacetylase activity / paranode region of axon / regulation of exit from mitosis / positive regulation of fatty acid biosynthetic process / Schmidt-Lanterman incisure / negative regulation of peptidyl-threonine phosphorylation / NAD-dependent protein lysine deacetylase activity / regulation of phosphorylation / protein acetyllysine N-acetyltransferase / myelination in peripheral nervous system / rDNA heterochromatin formation / protein deacetylation / positive regulation of oocyte maturation / histone deacetylase activity, NAD-dependent / juxtaparanode region of axon / Initiation of Nuclear Envelope (NE) Reformation / chromatin silencing complex / meiotic spindle / protein lysine deacetylase activity / regulation of myelination / response to redox state / positive regulation of DNA binding / histone deacetylase activity / histone acetyltransferase binding / negative regulation of fat cell differentiation / negative regulation of reactive oxygen species metabolic process / positive regulation of cell division / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / positive regulation of execution phase of apoptosis / glial cell projection / subtelomeric heterochromatin formation / heterochromatin / lipid catabolic process / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / substantia nigra development / negative regulation of autophagy / epigenetic regulation of gene expression / ubiquitin binding / meiotic cell cycle / negative regulation of protein catabolic process / autophagy / spindle / histone deacetylase binding / mitotic spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / heterochromatin formation / myelin sheath / chromosome / growth cone / cellular response to oxidative stress / midbody / perikaryon / cellular response to hypoxia / DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / chromosome, telomeric region / regulation of cell cycle / innate immune response / cell division / negative regulation of DNA-templated transcription / centrosome / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sirtuin, class I / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
: / ACETATE ION / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWirawan, R. / Frei, M. / Heider, A. / Papenkordt, N. / Friedrich, F. / Wein, T. / Jung, M. / Groll, M. / Huber, E.M. / Bracher, F.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)503267011 Germany
German Research Foundation (DFG)325871075 (SFB1309) Germany
CitationJournal: To Be Published
Title: Enhancing the potency of sirtuin 2 inhibitors through rational functional group modulations targeting NAD+ co-factor interactions
Authors: Wirawan, R. / Frei, M. / Heider, A. / Papenkordt, N. / Friedrich, F. / Wein, T. / Jung, M. / Groll, M. / Huber, E.M. / Bracher, F.
History
DepositionJul 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,36511
Polymers34,1771
Non-polymers1,18710
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint17 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.900, 73.710, 55.860
Angle α, β, γ (deg.)90.00, 94.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NAD-dependent protein deacetylase sirtuin-2 / NAD-dependent protein defatty-acylase sirtuin-2 / Regulatory protein SIR2 homolog 2 / SIR2-like protein 2


Mass: 34177.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2, SIR2L, SIR2L2 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): DE3
References: UniProt: Q8IXJ6, protein acetyllysine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 251 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1JLL / ~{N}-[4-[[3-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]phenyl]methoxy]-2-iodanyl-phenyl]-1-methyl-pyrazole-4-carboxamide


Mass: 628.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25IN6O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M sodium acetate 17 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0596 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0596 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 49669 / % possible obs: 96.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.47
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 8828 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.195 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18722 2483 5 %RANDOM
Rwork0.15608 ---
obs0.15765 47182 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.596 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å20.05 Å2
2--0.16 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: 1 / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 70 241 2620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132426
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152308
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.6523258
X-RAY DIFFRACTIONr_angle_other_deg1.2041.5775336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10821.849119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37915423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6971515
X-RAY DIFFRACTIONr_chiral_restr0.0570.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02541
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_it0.8231.7531158
X-RAY DIFFRACTIONr_mcbond_other0.8171.7491156
X-RAY DIFFRACTIONr_mcangle_it1.1492.6211441
X-RAY DIFFRACTIONr_mcangle_other1.1492.6231442
X-RAY DIFFRACTIONr_scbond_it0.9982.0461268
X-RAY DIFFRACTIONr_scbond_other0.9982.0471269
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2922.9811818
X-RAY DIFFRACTIONr_long_range_B_refined2.32321.8592780
X-RAY DIFFRACTIONr_long_range_B_other2.32321.8692781
X-RAY DIFFRACTIONr_rigid_bond_restr0.45834734
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 178 -
Rwork0.285 3386 -
obs--93.84 %

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