Structure of PDB 4zh4 Chain D Binding Site BS01

Receptor Information

>4zh4 Chain D (length=1151) Species: 83333 (Escherichia coli K-12)

LKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLF
CARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIEL
ASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQ
QILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNE
TNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDG
GRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALL
DNGRRGRAITGSNKRPLKSLADKRVDYSGRSVITVGPYLRLHQCGLPKKM
ALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVL
LNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPL
TLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKG
EGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDT
TVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFAD
QIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGL
VTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSI
YMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQY
FISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMM
TPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLL
EENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQS
IGEPGTQLTTGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRL
VITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRG
VHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFL
EGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASF
QETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAA
G

Ligand information

• Ligand ID: 4OE
• InChI: InChI=1S/C16H9F5N2/c17-11-4-1-9(2-5-11)15-12(8-22-23-15)10-3-6-14(18)13(7-10)16(19,20)21/h1-8H,(H,22,23)
• InChIKey: MQERCRUBCCKCNG-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: FC(c1c(ccc(c1)c2cnnc2c3ccc(F)cc3)F)(F)F
  OpenEye OEToolkits 1.9.2: c1cc(ccc1c2c(cn[nH]2)c3ccc(c(c3)C(F)(F)F)F)F
  CACTVS 3.385: Fc1ccc(cc1)c2[nH]ncc2c3ccc(F)c(c3)C(F)(F)F
• Formula: C16 H9 F5 N2
• Name: 5-(4-fluorophenyl)-4-[4-fluoro-3-(trifluoromethyl)phenyl]-1H-pyrazole
• ZINC: ZINC000000027354
• PDB chain: 4zh4 Chain C Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4zh4 Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles.
• Resolution: 3.993 Å
• Binding residue (original residue number in PDB): P750 I755 F773
• Binding residue (residue number reindexed from 1): P728 I733 F751
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.22,IC50=60uM

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:0005515 protein binding
• 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
• 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:4zh4, PDBe:4zh4, PDBj:4zh4
• PDBsum: 4zh4
• PubMed: 26190576
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)