Structure of PDB 8dg7 Chain A Binding Site BS05

Receptor Information
>8dg7 Chain A (length=1635) Species: 7227 (Drosophila melanogaster) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HTTVFTPRDFQVELLATAYERNTIICLGHRSSKEFIALKLLQELSRRARR
HGRVSVYLSCEVGTSTEPCSIYTMLTHLTDLRVWQEQPDMQIPFDHCWTD
YHVSILRPEGFLYLLETRELLLSRVELIVLEDCHDSAVYQRIRPLFENHI
MPAPPADRPRILGLAGPLHSAGCELQQLSAMLATLEQSVLCQIESASDIV
TVLRYCSRPHEYIVQCAPFEMDELSLVLADVLNTHKSFLLDHRYDPDPLN
VINSLLVVLHEMGPWCTQRAAHHFYQCNEKLKVKTPHERHYLLYCLVSTA
LIQLYSLCEHAFHRHLSRQTIERYSSPKVRRLLQTLRCFKTLCALIYCNQ
NHTARVLFELLAEISRRDPDLKFLRCQYTTDRVADPTTEPKEAELEHRRQ
EEVLKRFRMHDCNVLIGTSVLEEGIDVPKCNLVVRWDPPTTYRSYVQCKG
RARAAPAYHVILVAPSYKSPTVGSVQLTDRSHRYICATSLASTTKDLVHQ
MAQYREIEQMLLSKCANTEPPEQEQCEAERFSACLAAYRPKPHLLTGASV
DLGSAIALVNKYCARLPSDTFTKLTALWRCTRNERAGVTLFQYTLRLPIN
SPLKHDIVGLPMPTQTLARRLAALQACVELHRIGELDDQLQPIGKEGFRA
LEPDWECFELEPEDEQIVQLSDEPRPGTTKRRQYYYKRIASEFCDCRPVA
GAPCYLYFIQLTLQCPIPEEQNTRGRKIYPPEDAQQGFGILTTKRIPKLS
AFSIFTRSGEVKVSLELAKERVILTSEQIVCINGFLNYTFTNVLRLQKFL
MLFDPDSTENCVFIVPTVKAPAGGKHIDWQFLELIQANGNTMPRAVPDEE
RQAQPFDPQRFQDAVVMPWYRNQDQPQYFYVAEICPHLSPLSCFPGDNYR
TFKHYYLVKYGLTIQNTSQPLLDVDHTSARLNFLTPRYVNRKGVALPTSS
EETKRAKRENLEQKQILVPELCTVHPFPASLWRTAVCLPCILYRINGLLL
ADDIRKQVSADLGLGRQQIFEWPMLDFGWRQKQLSIIQATNANERQYQQT
KNLLIGFNFKHERYEESIAKLKTEIESGGMLVPHDQQLVVSMMELLKQLL
PYVLAKKLGDRRELLLSDLVELNADWVARHEQETYNVMGDSFDNYNDHHA
GFSFDRQPDLVGHPGPSPSIILQALTMSNANDGINLERLETIGDSFLKYA
ITTYLYITYENVHEGKLSHLRSKQVANLNLYRLGRRKRLGEYMIATKFEP
HDNWLPPCYYVPKELEKALKLADLLDIKNLSSVQICEMVDFSCFIPYNLV
SQHSIPDKSIADCVEALIGAYLIECGPRGALLFMAWLGVRVLPITRQLDG
GNQEQRIPGSTKPNAENVVTVYGAWPTPRSPLLHFAPNATEELDQLLSGF
EEFEESLGYKFRDRSYLLQAMTHASYTPNRLTDCYQRLEFLGDAVLDYLI
TRHLYEDPRQHSPGALTDLRSALVNNTIFASLAVRHGFHKFFRHLSPGLN
DVIDRFVRIQQENGHCIDDAEDVEVPKALGDVFESIAGAIFLDSNMSLDV
VWHVYSNMMSPEIEQFSNSVPKSPIRELLELEPETAKFGKPEKLADGRRV
RVTVDVFCKGTFRGIGRNYRIAKCTAAKCALRQLK
Ligand information
Ligand IDU5P
InChIInChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyDJJCXFVJDGTHFX-XVFCMESISA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H13 N2 O9 P
NameURIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL214393
DrugBankDB03685
ZINCZINC000002123545
PDB chain8dg7 Chain E Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8dg7 Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB.
Resolution3.32 Å
Binding residue
(original residue number in PDB)		R994 R1027 D1195 R1200
Binding residue
(residue number reindexed from 1)		R724 R757 D925 R930
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.26.3: ribonuclease III.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003727 single-stranded RNA binding
GO:0004386 helicase activity
GO:0004519 endonuclease activity
GO:0004521 RNA endonuclease activity
GO:0004525 ribonuclease III activity
GO:0004530 deoxyribonuclease I activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016891 RNA endonuclease activity, producing 5'-phosphomonoesters
GO:0046872 metal ion binding
GO:0070883 pre-miRNA binding
Biological Process
GO:0006309 apoptotic DNA fragmentation
GO:0006396 RNA processing
GO:0007279 pole cell formation
GO:0007294 germarium-derived oocyte fate determination
GO:0007367 segment polarity determination
GO:0030422 siRNA processing
GO:0030727 germarium-derived female germ-line cyst formation
GO:0031047 regulatory ncRNA-mediated gene silencing
GO:0031054 pre-miRNA processing
GO:0033227 dsRNA transport
GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing
GO:0035196 miRNA processing
GO:0042078 germ-line stem cell division
GO:0042594 response to starvation
GO:0045448 mitotic cell cycle, embryonic
GO:0048813 dendrite morphogenesis
GO:0070922 RISC complex assembly
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016442 RISC complex
GO:0070578 RISC-loading complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8dg7, PDBe:8dg7, PDBj:8dg7
PDBsum8dg7
PubMed36182693
UniProtQ9VCU9|DCR1_DROME Endoribonuclease Dcr-1 (Gene Name=Dcr-1)

[Back to BioLiP]