Structure of PDB 8dh4 Chain E Binding Site BS04

Receptor Information
>8dh4 Chain E (length=819) Species: 10760 (Escherichia phage T7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
INIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRK
MFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVAFQFLQEIKPE
AVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHF
KKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHV
GVRCIEMLIESTLAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITG
GGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKK
VLAVANVITKWKHCPVEDIPAIAWKRAAAAVYRKDKARKSRRISLEFMLE
QANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIG
KEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWA
EQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDE
VGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTG
EISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLED
TIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAA
KLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLG
QDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSF
GTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPAL
PAKGNLNLRDILESDFAFA
Ligand information
Ligand IDS96
InChIInChI=1S/C15H18N3O13P3S/c19-12-9(6-28-33(24,25)31-34(26,27)30-32(21,22)23)29-15(13(12)20)18-7-17-11-8(3-4-16-14(11)18)10-2-1-5-35-10/h1-5,7,9,12-13,15,19-20H,6H2,(H,24,25)(H,26,27)(H2,21,22,23)/t9-,12-,13-,15-/m1/s1
InChIKeySAOUNFXHOUBCDP-QGMIFYJMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[C@@H]1[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[C@H]([C@@H]1O)n2cnc3c(ccnc23)c4sccc4
CACTVS 3.385O[CH]1[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[CH]([CH]1O)n2cnc3c(ccnc23)c4sccc4
OpenEye OEToolkits 2.0.7c1cc(sc1)c2ccnc3c2ncn3C4C(C(C(O4)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 2.0.7c1cc(sc1)c2ccnc3c2ncn3C4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(C(O)C1O)n1cnc2c(ccnc21)c1cccs1
FormulaC15 H18 N3 O13 P3 S
Name(7P)-3-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-7-(thiophen-2-yl)-3H-imidazo[4,5-b]pyridine
ChEMBL
DrugBank
ZINC
PDB chain8dh4 Chain E Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8dh4 Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		Y571 R627 K631 M635 Y639
Binding residue
(residue number reindexed from 1)		Y518 R574 K578 M582 Y586
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0006351 DNA-templated transcription
GO:0019083 viral transcription
GO:0039695 DNA-templated viral transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8dh4, PDBe:8dh4, PDBj:8dh4
PDBsum8dh4
PubMed36635281
UniProtP00573|RPOL_BPT7 T7 RNA polymerase (Gene Name=1)

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