Structure of PDB 4yfn Chain D Binding Site BS04

Receptor Information
>4yfn 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
DNGRRGRAITGSNKRPLKSLADMIKGKQRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWD
ILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNAD
FDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGL
YYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN
GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYR
ILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRD
GQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPIT
ANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVT
EDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPR
NTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIIN
KGEAIGVIAAQSIGEPGTQLTTGGLPRVADLFEARRPKEPAILAEISGIV
SFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDG
PEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRK
ATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKAS
LATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGY
AYHQDRMRRRAAG
Ligand information
Ligand ID4C2
InChIInChI=1S/C22H23F3N4O5S/c1-12-21(13(2)34-27-12)35(32,33)28-17-18(20(31)19(17)30)29-9-7-16(8-10-29)26-11-14-3-5-15(6-4-14)22(23,24)25/h3-6,16,26,28H,7-11H2,1-2H3
InChIKeyWFHJESWCVOQIPR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1onc(C)c1[S](=O)(=O)NC2=C(N3CCC(CC3)NCc4ccc(cc4)C(F)(F)F)C(=O)C2=O
ACDLabs 12.01C=2(NS(c1c(noc1C)C)(=O)=O)C(C(=O)C=2N3CCC(CC3)NCc4ccc(cc4)C(F)(F)F)=O
OpenEye OEToolkits 1.9.2Cc1c(c(on1)C)S(=O)(=O)NC2=C(C(=O)C2=O)N3CCC(CC3)NCc4ccc(cc4)C(F)(F)F
FormulaC22 H23 F3 N4 O5 S
NameN-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide
ChEMBLCHEMBL3427515
DrugBank
ZINCZINC000221806520
PDB chain4yfn 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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PDB4yfn 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.
Resolution3.817 Å
Binding residue
(original residue number in PDB)		A1323 V1351 I1352
Binding residue
(residue number reindexed from 1)		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:4yfn, PDBe:4yfn, PDBj:4yfn
PDBsum4yfn
PubMed25798859
UniProtA7ZUK2|RPOC_ECO24 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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