Structure of PDB 8efk Chain A Binding Site BS03

Receptor Information
>8efk Chain A (length=598) 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
LHLPFSTTKDILEKLRPLHPLPGVILEWRRITNALTKVVFPLQREKQYHP
TLAMDRIYPIAQTHTATGRVSFTEPNIQNVPKDFEICMAFSVSMRHAFVP
FSGGMILAADYSQLELRVLAHLSKDQRLLQVLNGGADVFRCIAAEWKGVD
PETVNDSLRQQAKQICYGIIYGMGAKSLGEQMGVEENDAACYIESFKARY
KGINAFLKETVKNCIKNGYVQTLMGRRRYLPGISNTNTHIKAHAERQAVN
TTVQGSAADIVKLATVNIQKRLRKTYPTAPLSHQHTLRGAFFVLQLHDEL
IYETREEDLIQVAQIVKREMESAVKLYVKLKAKVKVGPSWGNLQDLDL
Ligand information
Ligand IDDDS
InChIInChI=1S/C10H16N5O11P3/c11-9-8-10(13-4-12-9)15(5-14-8)7-2-1-6(24-7)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h4-7H,1-3H2,(H,19,20)(H,21,22)(H2,11,12,13)(H2,16,17,18)/t6-,7+/m0/s1
InChIKeyOAKPWEUQDVLTCN-NKWVEPMBSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[C@H]3CC[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3CC[C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3CCC(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N
FormulaC10 H16 N5 O11 P3
Name2',3'-dideoxyadenosine triphosphate
ChEMBLCHEMBL1383
DrugBankDB02189
ZINCZINC000012501706
PDB chain8efk Chain A Residue 2802 [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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PDB8efk Structural basis of DNA polymerase theta mediated DNA end joining.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		Q2466 E2468 R2512 K2516 Q2517 Y2520 Y2524
Binding residue
(residue number reindexed from 1)		Q363 E365 R409 K413 Q414 Y417 Y421
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:8efk, PDBe:8efk, PDBj:8efk
PDBsum8efk
PubMed36583344
UniProtA0A4W6BKE5

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