Structure of PDB 5tmf Chain D Binding Site BS01

Receptor Information
>5tmf Chain D (length=1504) 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
VALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLF
RAEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKG
QPLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHM
NVVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVY
PFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYD
IDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRA
FLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRN
NRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLR
SLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALE
LFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVL
LNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPL
SSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKG
AGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALL
AVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQ
LDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGI
DDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTE
KVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGE
TFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDV
THEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAR
EVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVC
QKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAAD
ITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSK
EYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEE
IQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVE
ALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAA
IAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKE
AVEA
Ligand information
Ligand IDNE6
InChIInChI=1S/C23H31NO6/c1-6-9-15(2)11-12-17(4)21(26)20-18(25)14-19(30-22(20)27)16(3)10-7-8-13-24-23(28)29-5/h11-14,16,20H,6-10H2,1-5H3/b15-11+,17-12+,24-13+/t16-,20?/m1/s1
InChIKeyLTDLIPXLSBMTFP-FSAISGGASA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCC(C)=CC=C(C)C(=O)[CH]1C(=O)OC(=CC1=O)[CH](C)CCCC=NC(=O)OC
CACTVS 3.341CCCC(/C)=C/C=C(C)/C(=O)[C@H]1C(=O)OC(=CC1=O)[C@H](C)CCCC=NC(=O)OC
OpenEye OEToolkits 1.5.0CCC/C(=C/C=C(\C)/C(=O)C1C(=O)C=C(OC1=O)[C@H](C)CCC\C=N\C(=O)OC)/C
ACDLabs 10.04O=C(\C(=C\C=C(/C)CCC)C)C1C(=O)C=C(OC1=O)C(C)CCC\C=N\C(=O)OC
OpenEye OEToolkits 1.5.0CCCC(=CC=C(C)C(=O)C1C(=O)C=C(OC1=O)C(C)CCCC=NC(=O)OC)C
FormulaC23 H31 N O6
Namemethyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2,4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate
ChEMBL
DrugBankDB08266
ZINC
PDB chain5tmf Chain C Residue 1201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5tmf On the validation of crystallographic symmetry and the quality of structures.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		F614 L619 K1463 I1467
Binding residue
(residue number reindexed from 1)		F613 L618 K1462 I1466
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: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:5tmf, PDBe:5tmf, PDBj:5tmf
PDBsum5tmf
PubMed25352397
UniProtQ8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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