Structure of PDB 4yfx Chain D Binding Site BS04

Receptor Information
>4yfx Chain D (length=1166) 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]
LKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLF
CARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIEL
ASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQ
QILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNE
TNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDG
GRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALL
DNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITV
GPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAV
VWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAY
NADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVV
LGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEK
DANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNT
CYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEA
EAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVI
NRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIET
PITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDL
VVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADIL
VPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGH
IINKGEAIGVIAAQSIGEPGTQLTTGGLPRVADLFEARRPKEPAILAEIS
GIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVI
SDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQM
LRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGIT
KASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAG
TGYAYHQDRMRRRAAG
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)		K332 G333 L342 G344 K345 K1348 I1352
Binding residue
(residue number reindexed from 1)		K325 G326 L335 G337 K338 K1138 I1142
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
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
UniProtA7ZUK2|RPOC_ECO24 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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