Structure of PDB 4z6d Chain A Binding Site BS05

Receptor Information
>4z6d Chain A (length=327) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSG
AEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGI
GPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEML
QMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESQP
KLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIR
LIPKDQYYCGVLYFTGSDIFAKNMRAHALEKGFTINEYTIRPLGVTGVAG
EPLPVDSEKDIFDYIQWKYREPKDRSE
Ligand information
Ligand ID1FZ
InChIInChI=1S/C10H18N3O13P3/c1-5-3-13(10(16)11-9(5)15)8-2-6(14)7(25-8)4-24-27(17,18)12-28(19,20)26-29(21,22)23/h3,6-8,14H,2,4H2,1H3,(H,11,15,16)(H2,21,22,23)(H3,12,17,18,19,20)/t6-,7+,8+/m0/s1
InChIKeyYRKUYVYMPXAOAT-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.370CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H18 N3 O13 P3
Name5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
ChEMBL
DrugBank
ZINCZINC000013455017
PDB chain4z6d Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4z6d Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase beta.
Resolution2.51 Å
Binding residue
(original residue number in PDB)		S180 R183 S188 G189 D190 Y271 D276
Binding residue
(residue number reindexed from 1)		S174 R177 S182 G183 D184 Y263 D268
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D190 D192 D256
Catalytic site (residue number reindexed from 1) D184 D186 D248
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:4z6d, PDBe:4z6d, PDBj:4z6d
PDBsum4z6d
PubMed29301983
UniProtP06746|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)

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