Structure of PDB 4xsx Chain D Binding Site BS01

Receptor Information
>4xsx 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 ID42S
InChIInChI=1S/C14H11F3N2O/c15-14(16,17)11-6-4-5-10(9-11)13(19-20)18-12-7-2-1-3-8-12/h1-9,20H,(H,18,19)
InChIKeySFPWZRCGYUTPNJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1ccc(cc1)NC(=NO)c2cccc(c2)C(F)(F)F
OpenEye OEToolkits 1.9.2c1ccc(cc1)N/C(=N\O)/c2cccc(c2)C(F)(F)F
CACTVS 3.385O\N=C(/Nc1ccccc1)c2cccc(c2)C(F)(F)F
ACDLabs 12.01FC(F)(F)c2cccc(C(=N\O)\Nc1ccccc1)c2
CACTVS 3.385ON=C(Nc1ccccc1)c2cccc(c2)C(F)(F)F
FormulaC14 H11 F3 N2 O
NameN'-hydroxy-N-phenyl-3-(trifluoromethyl)benzenecarboximidamide
ChEMBLCHEMBL501382
DrugBank
ZINCZINC000004695447
PDB chain4xsx Chain C Residue 1401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4xsx CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.
Resolution3.708 Å
Binding residue
(original residue number in PDB)		P750 I755 L770 F773
Binding residue
(residue number reindexed from 1)		P743 I748 L763 F766
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.00,IC50~10uM
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:4xsx, PDBe:4xsx, PDBj:4xsx
PDBsum4xsx
PubMed26195788
UniProtA7ZUK2|RPOC_ECO24 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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