Structure of PDB 3eql Chain C Binding Site BS01

Receptor Information
>3eql Chain C (length=1119) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRE
TFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQL
IHKDTGLIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTP
DPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVL
GYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKR
DKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKD
EVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLAR
LARGVRERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNP
LSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIG
LITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYMTATEEDRYTIAQAN
TPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFL
EHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED
GEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVR
KGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY
TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVK
PGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIV
VRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVA
KILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQR
YISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKL
GLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHM
VEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQ
EMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDVQ
TLDEKDNPVDIFEGLASKR
Ligand information
Ligand IDMXP
InChIInChI=1S/C23H31NO6/c1-5-6-10-16(2)12-13-17(3)21(26)20-19(25)15-18(30-22(20)27)11-8-7-9-14-24-23(28)29-4/h9,12-15,25H,5-8,10-11H2,1-4H3,(H,24,28)/b14-9+,16-12+,17-13+
InChIKeyQBIHIGNYQFSBGW-NOTXRLOZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCC(=CC=C(C)C(=O)C1=C(C=C(OC1=O)CCCC=CNC(=O)OC)O)C
CACTVS 3.341CCCCC(C)=CC=C(C)C(=O)C1=C(O)C=C(CCCC=CNC(=O)OC)OC1=O
CACTVS 3.341CCCC/C(C)=C/C=C(C)/C(=O)C1=C(O)C=C(CCC\C=C\NC(=O)OC)OC1=O
OpenEye OEToolkits 1.5.0CCCC/C(=C/C=C(\C)/C(=O)C1=C(C=C(OC1=O)CCC\C=C\NC(=O)OC)O)/C
ACDLabs 10.04O=C(C1=C(O)C=C(OC1=O)CCC\C=C\NC(=O)OC)\C(=C\C=C(/C)CCCC)C
FormulaC23 H31 N O6
NameMyxopyronin B;
methyl [(1E)-5-{3-[(2E,4E)-2,5-dimethylnona-2,4-dienoyl]-4-hydroxy-2-oxo-2H-pyran-6-yl}pent-1-en-1-yl]carbamate
ChEMBLCHEMBL184023
DrugBankDB08226
ZINCZINC000028382402
PDB chain3eql Chain D Residue 1527 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3eql Transcription inactivation through local refolding of the RNA polymerase structure.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		E1034 W1038 S1084 L1088
Binding residue
(residue number reindexed from 1)		E1034 W1038 S1084 L1088
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.30,IC50=4.99uM
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:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
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:3eql, PDBe:3eql, PDBj:3eql
PDBsum3eql
PubMed18946472
UniProtQ8RQE9|RPOB_THET8 DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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