Structure of PDB 4yfk Chain D Binding Site BS05

Receptor Information
>4yfk Chain D (length=1163) 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
DNGRRGRAITGSNKRPLKSLADMIKGKFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWD
ILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNAD
FDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGL
YYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN
GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYR
ILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRD
GQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPIT
ANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVT
EDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPR
NTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIIN
KGEAIGVIAAQSIGEPGTQLTTGGLPRVADLFEARRPKEPAILAEISGIV
SFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDG
PEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRK
ATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKAS
LATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGY
AYHQDRMRRRAAG
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 D 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 K345 A1323 V1351 I1352
Binding residue
(residue number reindexed from 1)		L332 K335 A1110 V1138 I1139
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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