Structure of PDB 3dxj Chain C Binding Site BS01

Receptor Information
>3dxj Chain C (length=1119) Species: 300852 (Thermus thermophilus HB8) [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 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 chain3dxj Chain D Residue 1529 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dxj The RNA polymerase "switch region" is a target for inhibitors.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		V1037 W1038 E1041
Binding residue
(residue number reindexed from 1)		V1037 W1038 E1041
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.22,Kd=0.6uM
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:3dxj, PDBe:3dxj, PDBj:3dxj
PDBsum3dxj
PubMed18957204
UniProtQ8RQE9|RPOB_THET8 DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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