Structure of PDB 4yfx Chain C Binding Site BS01

Receptor Information
>4yfx Chain C (length=1340) Species: 331111 (Escherichia coli O139:H28 str. E24377A) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAA
FRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRL
VIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRS
PGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRR
KLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETAS
FDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYI
DESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLR
VDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGR
MKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRR
IRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAV
KEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHP
THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE
IHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDY
MDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGT
GMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYN
LTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRV
AFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITA
DIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLL
RAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQ
LKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGL
TDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKV
YLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLG
VPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLG
ADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLG
DLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYS
LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRT
KMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE
Ligand information
Ligand ID4C4
InChIInChI=1S/C24H33NO6/c1-6-7-10-16(2)12-13-18(4)22(27)21-19(26)15-20(31-23(21)28)17(3)11-8-9-14-25-24(29)30-5/h9,12-15,17,26H,6-8,10-11H2,1-5H3,(H,25,29)/b14-9+,16-12+,18-13+/t17-/m1/s1
InChIKeySPQDIDVJAZFBRL-WXFBSNOUSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C=1(C(OC(=CC=1O)C(C)CC[C@H]=[C@H]NC(=O)OC)=O)C(=O)C(C)=[C@H]\C=C(/C)CCCC
OpenEye OEToolkits 1.7.6CCCC/C(=C/C=C(\C)/C(=O)C1=C(C=C(OC1=O)[C@H](C)CC/C=C/NC(=O)OC)O)/C
CACTVS 3.385CCCCC(C)=CC=C(C)C(=O)C1=C(O)C=C(OC1=O)[CH](C)CCC=CNC(=O)OC
OpenEye OEToolkits 1.7.6CCCCC(=CC=C(C)C(=O)C1=C(C=C(OC1=O)C(C)CCC=CNC(=O)OC)O)C
CACTVS 3.385CCCCC(/C)=C/C=C(C)/C(=O)C1=C(O)C=C(OC1=O)[C@H](C)CC/C=C/NC(=O)OC
FormulaC24 H33 N O6
NameMyxopyronin B
ChEMBLCHEMBL247042
DrugBank
ZINCZINC000095606603
PDB chain4yfx Chain D Residue 2004 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yfx X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein.
Resolution3.844 Å
Binding residue
(original residue number in PDB)		G1271 E1272 W1276 E1279 S1322 L1326
Binding residue
(residue number reindexed from 1)		G1269 E1270 W1274 E1277 S1320 L1324
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4yfx, PDBe:4yfx, PDBj:4yfx
PDBsum4yfx
PubMed25798859
UniProtA7ZUK1|RPOB_ECO24 DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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