Structure of PDB 8ef9 Chain A Binding Site BS03

Receptor Information
>8ef9 Chain A (length=599) Species: 8187 (Lates calcarifer) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TFSIIDVASDRRLFNTFIKEWKTKERYSLALACEKREHDSDGLVLIGLSV
CWGARDSYYISLQQVSERLGQVRSCLSRPGGVVVTYDIIQVYKTLVLSCG
ISLAGNCEDPKVACWLLDPGSEERTLPNMVTVYCPEELPLLDGLGSAHAH
CPRVRAATKSVLVHAVMNHLTGLLEKDSMLDLFRSIEMPSQVCLALLELN
GVGFSVEECERQKHVMQAKLTALESQAYNLAGHSFSLTSIDDIAQVLFLE
LHLPQFSTTKDILEKLRPLHPLPGVILEWRRITNALTKVVFPLQREKQYH
PTLAMDRIYPIAQTHTATGRVSFTEPNIQNVPKDFEICMAFSVSMRHAFV
PFSGGMILAADYSQLELRVLAHLSKDQRLLQVLNGGADVFRCIAAEWKGV
DPETVNDSLRQQAKQICYGIIYGMGAKSLGEQMGVEENDAACYIESFKAR
YKGINAFLKETVKNCIKNGYVQTLMGRRRYLPGISNTNTHIKAHAERQAV
NTTVQGSAADIVKLATVNIQKRLRKTYPTAPLSHQHTLRGAFFVLQLHDE
LIYETREEDLIQVAQIVKREMESAVKLYVKLKAKVKVGPSWGNLQDLDL
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 chain8ef9 Chain A Residue 2801 [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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PDB8ef9 Structural basis of DNA polymerase theta mediated DNA end joining.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R2382 Y2464 Q2466 L2467 E2468 F2492 R2512 K2516 Y2520 Y2524 D2664 K2699
Binding residue
(residue number reindexed from 1)		R320 Y362 Q364 L365 E366 F390 R410 K414 Y418 Y422 D549 K584
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8ef9, PDBe:8ef9, PDBj:8ef9
PDBsum8ef9
PubMed36583344
UniProtA0A4W6BKE5

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