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- PDB-3fcf: Complex of UNG2 and a fragment-based designed inhibitor -

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Basic information

Entry
Database: PDB / ID: 3fcf
TitleComplex of UNG2 and a fragment-based designed 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 superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / 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 superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / 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-FCF / THIOCYANATE ION / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 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: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0074
Polymers25,5441
Non-polymers4623
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.251, 69.260, 70.097
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-FCF / 3-[(1E,7E)-8-(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)-3,6-dioxa-2,7-diazaocta-1,7-dien-1-yl]benzoic acid


Mass: 346.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N4O6
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.06 Å3/Da / Density % sol: 40.15 %
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 0.003 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 0.003 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

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 2, 2007 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 15237 / % possible obs: 79.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.053 / Χ2: 3.286
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.83-1.91.70.1472382.11412.7
1.9-1.972.20.1247982.38442.5
1.97-2.062.60.113122.6268.9
2.06-2.173.40.08816792.82189
2.17-2.315.30.07618603.08398.5
2.31-2.486.50.06918753.09598.8
2.48-2.736.50.05918593.16196.6
2.73-3.136.30.05218493.3596.3
3.13-3.945.90.04718153.53392.4
3.94-505.60.04819524.00294.3

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→36.81 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.844 / SU ML: 0.104 / SU R Cruickshank DPI: 0.226 / SU Rfree: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 749 4.9 %RANDOM
Rwork0.198 ---
obs0.2 15197 80.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 60.43 Å2 / Biso mean: 23.692 Å2 / Biso min: 15.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.89 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.84→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 31 179 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211918
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.9442598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1925226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95123.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4215311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.884159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021501
X-RAY DIFFRACTIONr_nbd_refined0.1770.2906
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21255
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.29
X-RAY DIFFRACTIONr_mcbond_it0.3931.51148
X-RAY DIFFRACTIONr_mcangle_it0.68721818
X-RAY DIFFRACTIONr_scbond_it1.0073886
X-RAY DIFFRACTIONr_scangle_it1.6124.5780
LS refinement shellResolution: 1.84→1.885 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 11 -
Rwork0.229 154 -
all-165 -
obs--11.88 %

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