Structure of PDB 6cux Chain C Binding Site BS01

Receptor Information
>6cux Chain C (length=1339) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLE
AAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKL
RLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLH
RSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDR
RRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGET
ASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKD
YIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISET
LRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAV
GRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGN
RRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISA
AVKEFFGSSQLSQFMDQNNPLSEITHKRRILALGPGGLTAGFEVRDVHPT
HYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEI
HYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYM
DVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTG
MERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNL
TKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVA
FMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITAD
IPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLR
AIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQL
KQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLT
DEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVY
LAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGV
PSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGA
DVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGD
LPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSL
VTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTK
MYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE
Ligand information
Ligand IDKNG
InChIInChI=1S/C50H67NO19/c1-21-13-12-14-29(26(6)67-48(62)49(9,10)19-34(54)55)40(57)23(3)39(56)24(4)43(68-28(8)52)22(2)32(69-35-18-33-45(27(7)66-35)64-20-63-33)15-16-65-50(11)46(60)38-36-31(53)17-30(51-47(21)61)42(59)37(36)41(58)25(5)44(38)70-50/h13,15-17,22-24,26-27,29,32-33,35,39-40,43,45,53,56-59H,12,14,18-20H2,1-11H3,(H,51,61)(H,54,55)/b16-15+,21-13-/t22-,23+,24-,26+,27-,29-,32+,33+,35+,39-,40-,43-,45-,50+/m1/s1
InChIKeyRKRZBNCHQZDJPK-UAXKWEMASA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H]1O[C@H](C[C@@H]2OCO[C@H]12)O[C@H]3\C=C\O[C@@]4(C)Oc5c(C)c(O)c6c(O)c(NC(=O)\C(=C/CC[C@H]([C@H](C)OC(=O)C(C)(C)CC(O)=O)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]3C)C)cc(O)c6c5C4=O
OpenEye OEToolkits 1.7.6Cc1c(c2c3c(cc(c2O)NC(=O)/C(=C\CC[C@@H]([C@@H]([C@H]([C@H]([C@H]([C@@H]([C@@H]([C@H](/C=C/O[C@@]4(C(=O)c3c1O4)C)O[C@H]5C[C@H]6[C@@H]([C@H](O5)C)OCO6)C)OC(=O)C)C)O)C)O)[C@H](C)OC(=O)C(C)(C)CC(=O)O)/C)O)O
OpenEye OEToolkits 1.7.6Cc1c(c2c3c(cc(c2O)NC(=O)C(=CCCC(C(C(C(C(C(C(C(C=COC4(C(=O)c3c1O4)C)OC5CC6C(C(O5)C)OCO6)C)OC(=O)C)C)O)C)O)C(C)OC(=O)C(C)(C)CC(=O)O)C)O)O
ACDLabs 12.01c1(c3c(c(c6c2C(C(C)(OC=CC(C(C(C(C(C(C(C(CCC=C(C(=O)Nc1cc(c23)O)C)C(OC(C(C)(C)CC(=O)O)=O)C)O)C)O)C)OC(C)=O)C)OC5CC4C(OCO4)C(C)O5)O6)=O)C)O)O
CACTVS 3.385C[CH]1O[CH](C[CH]2OCO[CH]12)O[CH]3C=CO[C]4(C)Oc5c(C)c(O)c6c(O)c(NC(=O)C(=CCC[CH]([CH](C)OC(=O)C(C)(C)CC(O)=O)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]3C)C)cc(O)c6c5C4=O
FormulaC50 H67 N O19
NameKanglemycin A;
4-{(1S)-1-[(1S,2S,12S,16S,17R,18S,19R,20R,21S,22R,23S,24E)-21-(acetyloxy)-23-[(2,6-dideoxy-3,4-O-methylidene-beta-D-ribo-hexopyranosyl)oxy]-1,5,6,9,17,19-hexahydroxy-2,4,12,18,20,22-hexamethyl-11-oxo-1,2-dihydro-2,7-(epoxypentadec[1]enoimino)naphtho[2,1-b]furan-16-yl]ethoxy}-3,3-dimethyl-4-oxobutanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6cux Chain C Residue 2001 [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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PDB6cux Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis.
Resolution4.104 Å
Binding residue
(original residue number in PDB)		R143 S508 S509 Q510 S512 Q513 F514 D516 R529 L531 R687
Binding residue
(residue number reindexed from 1)		R143 S508 S509 Q510 S512 Q513 F514 D516 R529 L531 R684
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: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:6cux, PDBe:6cux, PDBj:6cux
PDBsum6cux
PubMed30244835
UniProtP0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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