Structure of PDB 8vfd Chain A Binding Site BS04
Receptor Information
>8vfd Chain A (length=323) Species:
9606
(Homo sapiens) [
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PQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSG
AEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGI
GPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEML
QMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESQP
KLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKEYPHRRIDIRLIPK
DQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP
VDSEKDIFDYIQWKYREPKDRSE
Ligand information
Ligand ID
A1ACD
InChI
InChI=1S/C11H19N2O13P3/c1-6-3-13(11(16)12-10(6)15)9-2-7(14)8(25-9)4-24-27(17,18)5-28(19,20)26-29(21,22)23/h3,7-9,14H,2,4-5H2,1H3,(H,17,18)(H,19,20)(H,12,15,16)(H2,21,22,23)/t7-,8-,9-/m1/s1
InChIKey
AFUOLHFRDGMFSB-IWSPIJDZSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 2.0.7
CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.385
CC1=CN([C@H]2C[C@@H](O)[C@@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 12.01
O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC1OC(CC1O)N1C=C(C)C(=O)NC1=O
OpenEye OEToolkits 2.0.7
CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.385
CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
Formula
C11 H19 N2 O13 P3
Name
1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINC
PDB chain
8vfd Chain A Residue 402 [
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Receptor-Ligand Complex Structure
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PDB
8vfd
Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta.
Resolution
2.1 Å
Binding residue
(original residue number in PDB)
G179 S180 S188 G189 D190 D192 Y271 F272 G274 D276 N279
Binding residue
(residue number reindexed from 1)
G173 S174 S182 G183 D184 D186 Y259 F260 G262 D264 N267
Annotation score
1
Enzymatic activity
Enzyme Commision number
2.7.7.7
: DNA-directed DNA polymerase.
4.2.99.-
4.2.99.18
: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0003677
DNA binding
GO:0003684
damaged DNA binding
GO:0003887
DNA-directed DNA polymerase activity
GO:0003906
DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0005515
protein binding
GO:0008017
microtubule binding
GO:0016779
nucleotidyltransferase activity
GO:0016829
lyase activity
GO:0019899
enzyme binding
GO:0034061
DNA polymerase activity
GO:0046872
metal ion binding
GO:0051575
5'-deoxyribose-5-phosphate lyase activity
GO:0140078
class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological Process
GO:0001701
in utero embryonic development
GO:0006259
DNA metabolic process
GO:0006260
DNA replication
GO:0006261
DNA-templated DNA replication
GO:0006281
DNA repair
GO:0006284
base-excision repair
GO:0006287
base-excision repair, gap-filling
GO:0006290
pyrimidine dimer repair
GO:0006297
nucleotide-excision repair, DNA gap filling
GO:0006303
double-strand break repair via nonhomologous end joining
GO:0006915
apoptotic process
GO:0006954
inflammatory response
GO:0006974
DNA damage response
GO:0007435
salivary gland morphogenesis
GO:0008630
intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010332
response to gamma radiation
GO:0016445
somatic diversification of immunoglobulins
GO:0016446
somatic hypermutation of immunoglobulin genes
GO:0045471
response to ethanol
GO:0048535
lymph node development
GO:0048536
spleen development
GO:0048872
homeostasis of number of cells
GO:0051402
neuron apoptotic process
GO:0055093
response to hyperoxia
GO:0071707
immunoglobulin heavy chain V-D-J recombination
GO:0071897
DNA biosynthetic process
Cellular Component
GO:0005634
nucleus
GO:0005654
nucleoplasm
GO:0005737
cytoplasm
GO:0005874
microtubule
GO:0005876
spindle microtubule
GO:0032991
protein-containing complex
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Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:8vfd
,
PDBe:8vfd
,
PDBj:8vfd
PDBsum
8vfd
PubMed
38634780
UniProt
P06746
|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)
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