Structure of PDB 2d3y Chain A Binding Site BS02
Receptor Information
>2d3y Chain A (length=219) Species:
300852
(Thermus thermophilus HB8) [
Search protein sequence
] [
Download receptor structure
] [
Download structure with residue number starting from 1
] [
View receptor structure
]
MDREAFVQTLTACRLCPRLVAWREEVVGRKRAFRGEPYWARPVPGFGDPE
ARILLFGLAPGAHGSNRTGRPFTGDASGAFLYPLLHEAGLSSKPESLPGD
DLRLYGVYLTAAVRCAPPKNKPTPEELRACARWTEVELGLLPEVRVYVAL
GRIALEALLAHFGLRKSAHPFRHGAHYPLPGGRHLLASYHVSRQNTQTGR
LTREMFLEVLMEAKRLAGL
Ligand information
Ligand ID
DU
InChI
InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKey
JSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
Software
SMILES
CACTVS 3.341
O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04
O=C1NC(=O)N(C=C1)C2OC(C(O)C2)COP(=O)(O)O
OpenEye OEToolkits 1.5.0
C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.341
O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0
C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
Formula
C9 H13 N2 O8 P
Name
2'-DEOXYURIDINE-5'-MONOPHOSPHATE
ChEMBL
CHEMBL211312
DrugBank
DB03800
ZINC
ZINC000004228260
PDB chain
2d3y Chain A Residue 221 [
Download ligand structure
] [
Download structure with residue number starting from 1
] [
View ligand structure
]
Receptor-Ligand Complex Structure
Global view
Local view
Structure summary
[
Spin on
] [
Spin off
] [
Reset
]
[
High quality
] [
Low quality
]
[
White background
] [
Black background
]
[
Spin on
] [
Spin off
] [
Reset
]
[
High quality
] [
Low quality
]
[
White background
] [
Black background
]
PDB
2d3y
Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.
Resolution
1.55 Å
Binding residue
(original residue number in PDB)
F46 G47 D48 R103 L104
Binding residue
(residue number reindexed from 1)
F46 G47 D48 R103 L104
Annotation score
4
Enzymatic activity
Enzyme Commision number
3.2.2.-
Gene Ontology
Molecular Function
GO:0004844
uracil DNA N-glycosylase activity
GO:0016787
hydrolase activity
GO:0033958
DNA-deoxyinosine glycosylase activity
GO:0046872
metal ion binding
GO:0051536
iron-sulfur cluster binding
GO:0051539
4 iron, 4 sulfur cluster binding
GO:0097506
deaminated base DNA N-glycosylase activity
Biological Process
GO:0006281
DNA repair
GO:0006284
base-excision repair
View graph for
Molecular Function
View graph for
Biological Process
External links
PDB
RCSB:2d3y
,
PDBe:2d3y
,
PDBj:2d3y
PDBsum
2d3y
PubMed
17870091
UniProt
Q5SJ65
|UDGB_THET8 Type-5 uracil-DNA glycosylase (Gene Name=udgb)
[
Back to BioLiP
]