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

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Basic information

Entry
Database: PDB / ID: 3fcl
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-3FL / THIOCYANATE ION / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.7 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
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

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,24612
Polymers51,0882
Non-polymers1,15710
Water10,142563
1
A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1236
Polymers25,5441
Non-polymers5795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1236
Polymers25,5441
Non-polymers5795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.108, 43.387, 70.684
Angle α, β, γ (deg.)90.000, 90.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 25544.137 Da / Num. of mol.: 2
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-3FL / 3-{[(4-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}butyl)amino]methyl}benzoic acid


Mass: 346.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22N4O4
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.1 Å3/Da / Density % sol: 41.54 %

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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: Aug 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 44162 / % possible obs: 73.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.039 / Χ2: 2.706
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.57-1.631.30.7673432.3255.7
1.63-1.691.40.55716053.6927
1.69-1.771.60.32929873.40650.1
1.77-1.8620.1745922.33577.1
1.86-1.982.50.12358143.04196.6
1.98-2.132.50.07857432.55796.2
2.13-2.352.40.05357632.54396.4
2.35-2.682.50.03858502.40897.1
2.68-3.382.50.0358052.30996.1
3.38-502.40.03556603.41591.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.7→27.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.828 / SU B: 2.76 / SU ML: 0.091 / SU R Cruickshank DPI: 0.148 / SU Rfree: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2126 5.1 %RANDOM
Rwork0.189 ---
obs0.191 41799 88.58 %-
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: 84.86 Å2 / Biso mean: 26.993 Å2 / Biso min: 17.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.01 Å2
2---1.39 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 74 563 4279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213827
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9445184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2475452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45323.631179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91715610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0691517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022981
X-RAY DIFFRACTIONr_nbd_refined0.1960.21900
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2541
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.252
X-RAY DIFFRACTIONr_mcbond_it0.5071.52301
X-RAY DIFFRACTIONr_mcangle_it0.83923633
X-RAY DIFFRACTIONr_scbond_it1.32131767
X-RAY DIFFRACTIONr_scangle_it2.0464.51551
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.511 79 -
Rwork0.393 1647 -
all-1726 -
obs--49.5 %

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