Structure of PDB 4yfk Chain J Binding Site BS05

Receptor Information
>4yfk Chain J (length=1152) 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]
EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIW
FLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQY
LDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK
KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDL
NDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA
ITGSNKRPLKSLADMIKGKQGRNLLGKRVDYSGRSVITVGPYLRLHQCGL
PKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIRE
HPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAV
HVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCV
NAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTS
LKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTV
IFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQF
QSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVS
FNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLN
VLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHE
GIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQW
CDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVI
AAQSIGEPGTQLTGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKR
RLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRL
RGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSD
FLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAA
SFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRR
AA
Ligand information
Ligand ID4C6
InChIInChI=1S/C22H25N3O5S/c1-13-4-6-16(7-5-13)12-17-8-10-25(11-9-17)19-18(20(26)21(19)27)24-31(28,29)22-14(2)23-30-15(22)3/h4-7,17,24H,8-12H2,1-3H3
InChIKeyDJQHTHRCUXNHLQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1ccc(cc1)CC2CCN(CC2)C3=C(C(=O)C3=O)NS(=O)(=O)c4c(noc4C)C
CACTVS 3.385Cc1ccc(CC2CCN(CC2)C3=C(N[S](=O)(=O)c4c(C)onc4C)C(=O)C3=O)cc1
ACDLabs 12.01C4(NS(c1c(C)onc1C)(=O)=O)=C(N3CCC(Cc2ccc(cc2)C)CC3)C(=O)C4=O
FormulaC22 H25 N3 O5 S
Name3,5-dimethyl-N-{2-[4-(4-methylbenzyl)piperidin-1-yl]-3,4-dioxocyclobut-1-en-1-yl}-1,2-oxazole-4-sulfonamide
ChEMBLCHEMBL3427509
DrugBank
ZINCZINC000221806450
PDB chain4yfk Chain J Residue 2004 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yfk X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein.
Resolution3.571 Å
Binding residue
(original residue number in PDB)		L342 G344 A1323 I1352
Binding residue
(residue number reindexed from 1)		L324 G326 A1100 I1129
Annotation score1
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:4yfk, PDBe:4yfk, PDBj:4yfk
PDBsum4yfk
PubMed25798859
UniProtA7ZUK2|RPOC_ECO24 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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