Structure of PDB 4kn7 Chain C Binding Site BS01

Receptor Information
>4kn7 Chain C (length=1335) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVF
PIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYER
EAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFF
DSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPAT
IILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEA
NGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTG
ELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTN
DRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNR
SLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVG
EMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFG
SSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGR
VCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLS
AIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVST
QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERA
VAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYT
RSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPW
NGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNV
GEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFG
EKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAK
KDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEK
QNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVK
RRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRM
NIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQ
KVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTS
GQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQ
PLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKN
IVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE
Ligand information
Ligand ID1RM
InChIInChI=1S/C56H70N6O13/c1-31-14-12-15-32(2)55(69)59-46-50(67)42-41(45-53(46)74-40-17-13-16-39(44(40)58-45)71-28-11-10-20-60-22-24-61(25-23-60)26-27-62-21-19-57-30-62)43-52(36(6)49(42)66)75-56(8,54(43)68)72-29-18-38(70-9)33(3)51(73-37(7)63)35(5)48(65)34(4)47(31)64/h12-19,21,29-31,33-35,38,47-48,51,64-66H,10-11,20,22-28H2,1-9H3,(H,59,69)/b14-12+,29-18+,32-15?/t31-,33+,34+,35+,38-,47-,48+,51+,56-/m0/s1
InChIKeyBWDTVIVNIJMQGS-DORLTJSWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](C=CC=C(C(=O)NC(=C5C3=Nc6c(cccc6OCCCCN7CCN(CC7)CCn8ccnc8)O5)C2=O)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
CACTVS 3.370CO[C@H]1\C=C\O[C@@]2(C)Oc3c(C)c(O)c4C(=O)C(=C5Oc6cccc(OCCCCN7CCN(CC7)CCn8ccnc8)c6N=C5c4c3C2=O)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
CACTVS 3.370CO[CH]1C=CO[C]2(C)Oc3c(C)c(O)c4C(=O)C(=C5Oc6cccc(OCCCCN7CCN(CC7)CCn8ccnc8)c6N=C5c4c3C2=O)NC(=O)C(=CC=C[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]1C)C
ACDLabs 12.01O=C8c7c1OC8(OC=CC(OC)C(C)C(OC(=O)C)C(C)C(O)C(C)C(O)C(C=CC=C(C(=O)NC=2C(=O)c(c(O)c1C)c7C3=Nc6c(OC=23)cccc6OCCCCN5CCN(CCn4ccnc4)CC5)C)C)C
OpenEye OEToolkits 1.7.6Cc1c(c2c3c4c1OC(C4=O)(OC=CC(C(C(C(C(C(C(C(C=CC=C(C(=O)NC(=C5C3=Nc6c(cccc6OCCCCN7CCN(CC7)CCn8ccnc8)O5)C2=O)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
FormulaC56 H70 N6 O13
NameBenzoxazinorifamycin-2c
ChEMBL
DrugBank
ZINC
PDB chain4kn7 Chain C Residue 1401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4kn7 X-ray Crystal Structures of the Escherichia coli RNA Polymerase in Complex with Benzoxazinorifamycins.
Resolution3.686 Å
Binding residue
(original residue number in PDB)		Q513 F514 R529 S531 L533 R540 I572
Binding residue
(residue number reindexed from 1)		Q506 F507 R522 S524 L526 R533 I565
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.62,IC50=24nM
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:0005515 protein binding
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0006351 DNA-templated transcription
GO:0006352 DNA-templated transcription initiation
GO:0006879 intracellular iron ion homeostasis
GO:0009408 response to heat
GO:0031564 transcription antitermination
GO:0032784 regulation of DNA-templated transcription elongation
GO:0036460 cellular response to cell envelope stress
GO:0042128 nitrate assimilation
GO:0044780 bacterial-type flagellum assembly
GO:0046677 response to antibiotic
GO:0048870 cell motility
GO:0071973 bacterial-type flagellum-dependent cell motility
GO:0090605 submerged biofilm formation
GO:2000142 regulation of DNA-templated transcription initiation
Cellular Component
GO:0000345 cytosolic DNA-directed RNA polymerase complex
GO:0000428 DNA-directed RNA polymerase complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0008023 transcription elongation factor complex
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4kn7, PDBe:4kn7, PDBj:4kn7
PDBsum4kn7
PubMed23679862
UniProtP0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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