Structure of PDB 4fyd Chain A Binding Site BS04

Receptor Information
>4fyd Chain A (length=848) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDTFQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPR
EGKTPTDIHEEIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKV
LLPYQTPKSSRDTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLD
IKGADFNSSHCAVEVSVDKPQNITPTTTKTMPNLRCLSLSIQTLMNPKEN
KQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAALA
KQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRM
HDLNIPTFSSIGRRLRRTWPEKFGNMNHFFISDICSGRLICDIANEMGQS
LTPKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENIT
NCMISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFS
RNGFIVPDKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFT
TVDRNKEDIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTETDPH
KRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNT
RQLAESMNLLVVYGDTNSVMIDTGCDNYADAIKIGLGFKRLVNERYRLLE
IDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCPL
SRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINM
KLSKDPKAYPGGKNMPAVQVALRMRKAGRVVKAGSVITFVITKSVAERAH
ALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALG
Ligand information
Ligand IDDGT
InChIInChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyHAAZLUGHYHWQIW-KVQBGUIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H16 N5 O13 P3
Name2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL477486
DrugBankDB02181
ZINCZINC000008215755
PDB chain4fyd Chain A Residue 1301 [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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PDB4fyd Mechanism for priming DNA synthesis by yeast DNA Polymerase alpha
Resolution3.1 Å
Binding residue
(original residue number in PDB)		D864 S867 Y869 R917 N948 Y951 N998
Binding residue
(residue number reindexed from 1)		D483 S486 Y488 R536 N567 Y570 N617
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:1902975 mitotic DNA replication initiation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4fyd, PDBe:4fyd, PDBj:4fyd
PDBsum4fyd
PubMed23599895
UniProtP13382|DPOLA_YEAST DNA polymerase alpha catalytic subunit A (Gene Name=POL1)

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