Structure of PDB 3eql Chain D Binding Site BS03

Receptor Information
>3eql Chain D (length=1321) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQ
LLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDG
VALYRFASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGR
VEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHP
SRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGR
FATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDN
GRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVG
PQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIK
DEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCE
AFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD
IILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRET
SVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFAR
IVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDAL
KYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLT
DRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQ
IRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADT
ALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRL
RKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQ
EVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGT
QLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVRIE
ETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQ
LLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDP
GDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSW
LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFT
QVVDQKTLKAIEEARKEAVEA
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
Global viewLocal viewStructure summary

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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)		K610 Q611 L619 G620 K1463 I1467
Binding residue
(residue number reindexed from 1)		K426 Q427 L435 G436 K1279 I1283
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: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
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
UniProtQ8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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