Structure of PDB 4xsz Chain D Binding Site BS01

Receptor Information
>4xsz 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 ID42U
InChIInChI=1S/C22H23F4N5/c23-17-4-1-15(2-5-17)21-18(14-29-30-21)16-3-6-20(19(13-16)22(24,25)26)28-9-12-31-10-7-27-8-11-31/h1-6,13-14,27-28H,7-12H2,(H,29,30)
InChIKeyOXSJLZKYOPQBJE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC(F)(F)c4c(NCCN1CCNCC1)ccc(c3cnnc3c2ccc(F)cc2)c4
CACTVS 3.385Fc1ccc(cc1)c2n[nH]cc2c3ccc(NCCN4CCNCC4)c(c3)C(F)(F)F
OpenEye OEToolkits 1.9.2c1cc(ccc1c2c(c[nH]n2)c3ccc(c(c3)C(F)(F)F)NCCN4CCNCC4)F
FormulaC22 H23 F4 N5
Name4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]-N-[2-(piperazin-1-yl)ethyl]-2-(trifluoromethyl)aniline;
CBR-9393
ChEMBL
DrugBank
ZINCZINC000022450023
PDB chain4xsz 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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PDB4xsz CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.
Resolution3.683 Å
Binding residue
(original residue number in PDB)		K749 P750 I755 I774
Binding residue
(residue number reindexed from 1)		K742 P743 I748 I767
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.60,IC50=2.5uM
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:4xsz, PDBe:4xsz, PDBj:4xsz
PDBsum4xsz
PubMed26195788
UniProtA7ZUK2|RPOC_ECO24 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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