Structure of PDB 4zh2 Chain C Binding Site BS01

Receptor Information

>4zh2 Chain C (length=1340) Species: 83333 (Escherichia coli K-12)

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 ID: 4OB
• InChI: InChI=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)
• InChIKey: SFPWZRCGYUTPNJ-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: c1ccc(cc1)N=C(c2cccc(c2)C(F)(F)F)NO
  CACTVS 3.385: ONC(=Nc1ccccc1)c2cccc(c2)C(F)(F)F
  OpenEye OEToolkits 1.9.2: c1ccc(cc1)/N=C(\c2cccc(c2)C(F)(F)F)/NO
  ACDLabs 12.01: FC(c1cccc(c1)/C(NO)=N\c2ccccc2)(F)F
• Formula: C14 H11 F3 N2 O
• Name: N-hydroxy-N'-phenyl-3-(trifluoromethyl)benzenecarboximidamide
• ChEMBL: CHEMBL501382
• ZINC: ZINC000004695447
• PDB chain: 4zh2 Chain C Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4zh2 Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles.
• Resolution: 4.204 Å
• Binding residue (original residue number in PDB): P552 Y555 G640 E641 S642
• Binding residue (residue number reindexed from 1): P550 Y553 G638 E639 S640
• Annotation score: 1
• Binding affinity: PDBbind-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: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

External links

• PDB: RCSB:4zh2, PDBe:4zh2, PDBj:4zh2
• PDBsum: 4zh2
• PubMed: 26190576
• UniProt: P0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)