Structure of PDB 4xsz Chain C Binding Site BS01

Receptor Information
>4xsz Chain C (length=1340) 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]
YSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAA
FRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRL
VIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRS
PGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRR
KLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETAS
FDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYI
DESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLR
VDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGR
MKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRR
IRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAV
KEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHP
THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE
IHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDY
MDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGT
GMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYN
LTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRV
AFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITA
DIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLL
RAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQ
LKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGL
TDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKV
YLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLG
VPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLG
ADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLG
DLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYS
LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRT
KMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE
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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		D444 P552 Y555 E641 S642
Binding residue
(residue number reindexed from 1)		D442 P550 Y553 E639 S640
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:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0006351 DNA-templated transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4xsz, PDBe:4xsz, PDBj:4xsz
PDBsum4xsz
PubMed26195788
UniProtA7ZUK1|RPOB_ECO24 DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

[Back to BioLiP]