Structure of PDB 4qzd Chain A Binding Site BS06

Receptor Information
>4qzd Chain A (length=348) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKKISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASS
VLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERY
KSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYY
EDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDF
LITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKDHFQKCA
LILKLDHGRVHSGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRR
YATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA
Ligand information
Ligand IDDCT
InChIInChI=1S/C9H16N3O12P3/c10-7-3-4-12(9(13)11-7)8-2-1-6(22-8)5-21-26(17,18)24-27(19,20)23-25(14,15)16/h3-4,6,8H,1-2,5H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1
InChIKeyARLKCWCREKRROD-POYBYMJQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1CC(OC1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
OpenEye OEToolkits 1.5.0C1C[C@@H](O[C@@H]1CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@H]2CC[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2
FormulaC9 H16 N3 O12 P3
Name2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL1201384
DrugBank
ZINCZINC000013516800
PDB chain4qzd Chain A Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4qzd Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		G332 R336 G341 H342 D343 D345 G449 W450 G452 R454 E457
Binding residue
(residue number reindexed from 1)		G186 R190 G195 H196 D197 D199 G287 W288 G290 R292 E295
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D343 D345 D434
Catalytic site (residue number reindexed from 1) D197 D199 D272
Enzyme Commision number 2.7.7.31: DNA nucleotidylexotransferase.
3.1.11.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034061 DNA polymerase activity
Biological Process
GO:0006281 DNA repair

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Molecular Function
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Biological Process
External links
PDB RCSB:4qzd, PDBe:4qzd, PDBj:4qzd
PDBsum4qzd
PubMed25762590
UniProtP09838|TDT_MOUSE DNA nucleotidylexotransferase (Gene Name=Dntt)

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