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- PDB-3fck: Complex of UNG2 and a fragment-based design inhibitor -

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Basic information

Entry
Database: PDB / ID: 3fck
TitleComplex of UNG2 and a fragment-based design inhibitor
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / DNA REPAIR / URACIL / URACIL DNA GLYCOSYLASE / Alternative splicing / Disease mutation / DNA damage / Glycosidase / Host-virus interaction / Mitochondrion / Nucleus / Phosphoprotein / Transit peptide
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FCK / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsBianchet, M.A. / Chung, S. / Parker, J.B. / Amzel, L.M. / Stivers, J.T.
Citation
Journal: Nat.Chem.Biol. / Year: 2009
Title: Impact of linker strain and flexibility in the design of a fragment-based inhibitor
Authors: Chung, S. / Parker, J.B. / Bianchet, M. / Amzel, L.M. / Stivers, J.T.
#1: Journal: J.Am.Chem.Soc. / Year: 2005
Title: Uracil-directed ligand tethering: an efficient strategy for uracil DNA glycosylase (UNG) inhibitor development
Authors: Jiang, T.L. / Krosky, D.J. / Seiple, L. / Stivers, J.T.
#2: Journal: Nucleic Acids Res. / Year: 2006
Title: Mimicking damaged DNA with a small molecule inhibitor of human UNG2.
Authors: Krosky, D.J. / Bianchet, M.A. / Seiple, L. / Chung, S. / Amzel, L.M. / Stivers, J.T.
History
DepositionNov 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8902
Polymers25,5441
Non-polymers3461
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.180, 69.149, 70.037
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uracil-DNA glycosylase / / UDG


Mass: 25544.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNG, DGU, UNG1, UNG15 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P13051, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-FCK / 3-({[3-({[(1E)-(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methylidene]amino}oxy)propyl]amino}methyl)benzoic acid


Mass: 346.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 MICROLITER OF THE SOLUTION: 0.001 M UNG2 0.05 M TRIS-OAC pH 7.0, 0.15 M NACL 0.001 M DTT 0.005 M INHIBITOR, WAS MIXED WITH EQUAL AMOUNT OF THE SOLUTION CONTAINING 0.16 M KSCN AND 22% PEG ...Details: 1 MICROLITER OF THE SOLUTION: 0.001 M UNG2 0.05 M TRIS-OAC pH 7.0, 0.15 M NACL 0.001 M DTT 0.005 M INHIBITOR, WAS MIXED WITH EQUAL AMOUNT OF THE SOLUTION CONTAINING 0.16 M KSCN AND 22% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 22828 / % possible obs: 84.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.042 / Χ2: 2.268
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.63-1.691.40.5423842.30914.7
1.69-1.761.70.39714242.20953.6
1.76-1.842.10.20122201.65584.4
1.84-1.933.20.13226191.53798
1.93-2.0550.09426671.802100
2.05-2.215.10.06826482.05999.9
2.21-2.435.20.05126762.21699.9
2.43-2.795.20.0426952.23499.6
2.79-3.515.20.03427192.45799.3
3.51-504.90.0427763.36696.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→27.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.205 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.844 / SU B: 2.271 / SU ML: 0.078 / SU R Cruickshank DPI: 0.132 / SU Rfree: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1124 4.9 %RANDOM
Rwork0.195 ---
obs0.197 22779 85.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.18 Å2 / Biso mean: 25.738 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.64→27.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 25 210 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211871
X-RAY DIFFRACTIONr_angle_refined_deg1.011.9342538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2395221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34823.70889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98915304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.962158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021456
X-RAY DIFFRACTIONr_nbd_refined0.1930.2912
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.214
X-RAY DIFFRACTIONr_mcbond_it0.4781.51129
X-RAY DIFFRACTIONr_mcangle_it0.83721788
X-RAY DIFFRACTIONr_scbond_it1.2913851
X-RAY DIFFRACTIONr_scangle_it2.1054.5750
LS refinement shellResolution: 1.64→1.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.783 13 -
Rwork0.565 239 -
all-252 -
obs--13 %

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