Structure of PDB 1ynn Chain C Binding Site BS01

Receptor Information

>1ynn Chain C (length=1114) Species: 271 (Thermus aquaticus)

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 ID: RFP
• InChI: InChI=1S/C43H58N4O12/c1-21-12-11-13-22(2)42(55)45-33-28(20-44-47-17-15-46(9)16-18-47)37(52)30-31(38(33)53)36(51)26(6)40-32(30)41(54)43(8,59-40)57-19-14-29(56-10)23(3)39(58-27(7)48)25(5)35(50)24(4)34(21)49/h11-14,19-21,23-25,29,34-35,39,49-53H,15-18H2,1-10H3,(H,45,55)/b12-11+,19-14+,22-13-,44-20+/t21-,23+,24+,25+,29-,34-,35+,39+,43-/m0/s1
• InChIKey: JQXXHWHPUNPDRT-WLSIYKJHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](C=C\C=C(/C(=O)Nc(c2O)c(c3O)\C=N\N5CCN(CC5)C)\C)C)O)C)O)C)OC(=O)C)C)OC)C)O
  ACDLabs 10.04: O=C4c5c2c(O)c(\C=N\N1CCN(C)CC1)c3c(O)c2c(O)c(c5OC4(OC=CC(OC)C(C(OC(=O)C)C(C)C(O)C(C)C(O)C(C=CC=C(C(=O)N3)C)C)C)C)C
  CACTVS 3.341: CO[CH]1C=CO[C]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)C(=CC=C[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]1C)C)c(C=NN5CCN(C)CC5)c(O)c4c3C2=O
  CACTVS 3.341: CO[C@H]1\C=C\O[C@@]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)\C(=C/C=C/[C@H](C)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)C)c(\C=N\N5CCN(C)CC5)c(O)c4c3C2=O
  OpenEye OEToolkits 1.5.0: Cc1c(c2c3c4c1OC(C4=O)(OC=CC(C(C(C(C(C(C(C(C=CC=C(C(=O)Nc(c2O)c(c3O)C=NN5CCN(CC5)C)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
• Formula: C43 H58 N4 O12
• Name: RIFAMPICIN
• ChEMBL: CHEMBL374478
• DrugBank: DB01045
• ZINC: ZINC000169621223
• PDB chain: 1ynn Chain C Residue 1120

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ynn Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): Q390 Q393 F394 D396 R409 I452
• Binding residue (residue number reindexed from 1): Q390 Q393 F394 D396 R409 I452
• Annotation score: 1

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

External links

• PDB: RCSB:1ynn, PDBe:1ynn, PDBj:1ynn
• PDBsum: 1ynn
• PubMed: 15692574
• UniProt: Q9KWU7|RPOB_THEAQ DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)