Structure of PDB 1ynj Chain C Binding Site BS01

Receptor Information
>1ynj Chain C (length=1114) Species: 271 (Thermus aquaticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEIKRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKE
TFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQL
IHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTP
DPARPGRYIASIIPLPKRGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVL
GYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKK
DKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKD
EVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGLAR
LARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNP
LSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIG
LITSLAAYARVDALGFIRTPYRRVKNGVVTEEVVYMTASEEDRYTIAQAN
TPLEGDRIATDRVVARRRGEPVIVAPEEVEFMDVSPKQVFSLNTNLIPFL
EHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED
GEVVKVDGTRIAVRYEDGRLVEHPLRRYARSNQGTAFDQRPRVRVGQRVK
KGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY
TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVK
PGDILVGRTSFKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIV
VGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVA
KILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQR
YISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKL
GLVSPGKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHM
VEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQ
EMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPESFRVLVKELQALALDVQ
TLDEKDNPVDIFEG
Ligand information
Ligand IDSRN
InChIInChI=1S/C47H66O11/c1-30(17-14-15-23-44(50)51)27-31(2)47-40-26-25-34(54-47)18-10-6-5-7-11-19-35(48)46(53)43-28-36(49)32(3)37(56-43)21-16-22-38-33(4)41-29-42(55-38)39(57-41)20-12-8-9-13-24-45(52)58-40/h6,8-13,16,19-20,22,24-27,30,32-43,46-49,53H,5,7,14-15,17-18,21,23,28-29H2,1-4H3,(H,50,51)/b9-8-,10-6+,19-11+,20-12+,22-16+,24-13-,31-27+/t30-,32-,33+,34+,35+,36+,37-,38+,39-,40+,41-,42-,43-,46+,47+/m1/s1
InChIKeyOTABDKFPJQZJRD-QLGZCQHWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@H]1[C@H]2C\C=C\[C@H]3[C@@H]([C@H]4C[C@@H](O3)[C@H](O4)/C=C/C=C\C=C/C(=O)O[C@H]5C=C[C@H](C\C=C\CC\C=C\[C@@H]([C@@H]([C@H](O2)C[C@@H]1O)O)O)O[C@H]5/C(=C/[C@H](C)CCCCC(=O)O)/C)C
OpenEye OEToolkits 1.5.0CC1C2CC=CC3C(C4CC(O3)C(O4)C=CC=CC=CC(=O)OC5C=CC(CC=CCCC=CC(C(C(O2)CC1O)O)O)OC5C(=CC(C)CCCCC(=O)O)C)C
CACTVS 3.341C[CH](CCCCC(O)=O)C=C(C)[CH]1O[CH]2CC=CCCC=C[CH](O)[CH](O)[CH]3C[CH](O)[CH](C)[CH](CC=C[CH]4O[CH]5C[CH](O[CH]5C=CC=CC=CC(=O)O[CH]1C=C2)[CH]4C)O3
CACTVS 3.341C[C@H](CCCCC(O)=O)\C=C(/C)[C@@H]1O[C@H]2C\C=C\CC\C=C\[C@H](O)[C@H](O)[C@H]3C[C@H](O)[C@@H](C)[C@@H](C\C=C\[C@@H]4O[C@@H]5C[C@@H](O[C@@H]5\C=C\C=C/C=C\C(=O)O[C@H]1C=C2)[C@H]4C)O3
ACDLabs 10.04O=C2OC1C=CC(OC1C(=C/C(C)CCCCC(=O)O)/C)CC=CCCC=CC(O)C(O)C5OC(CC=CC4OC3CC(OC3C=CC=CC=C2)C4C)C(C)C(O)C5
FormulaC47 H66 O11
NameSORANGICIN A
ChEMBL
DrugBank
ZINCZINC000255256293
PDB chain1ynj Chain C Residue 1120 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ynj Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase
Resolution3.2 Å
Binding residue
(original residue number in PDB)		Q390 Q393 F394 D396 R409 S411 I452
Binding residue
(residue number reindexed from 1)		Q390 Q393 F394 D396 R409 S411 I452
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:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0006351 DNA-templated transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ynj, PDBe:1ynj, PDBj:1ynj
PDBsum1ynj
PubMed15692574
UniProtQ9KWU7|RPOB_THEAQ DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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