Structure of PDB 4oir Chain C Binding Site BS04

Receptor Information
>4oir Chain C (length=1112) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRE
TFPIEEGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTG
LIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPG
RYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQET
LARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAY
VYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPT
LRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVR
ERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRH
KRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLA
AYARVDELGFIRTPYRRVVGGVVTDEVVYMTATEEDRYTIAQANTPLEGN
RIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDAN
RALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKV
DGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLA
DGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIE
RYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILV
GRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRL
RRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVE
DMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIF
DGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPG
KTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMH
ARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLK
SDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKD
NPVDIFEGLASK
Ligand information
Ligand IDRFV
InChIInChI=1S/C37H49NO12/c1-16-11-10-12-17(2)36(46)38-23-15-24(40)26-27(32(23)44)31(43)21(6)34-28(26)35(45)37(8,50-34)48-14-13-25(47-9)18(3)33(49-22(7)39)20(5)30(42)19(4)29(16)41/h10-16,18-20,25,29-30,33,35,40-45H,1-9H3,(H,38,46)/b11-10+,14-13+,17-12-/t16-,18+,19+,20+,25-,29-,30+,33+,35+,37-/m0/s1
InChIKeyOUOULRWGQDSKTQ-ZVFQNIRDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c(c2c3c(cc(c2O)NC(=O)C(=CC=CC(C(C(C(C(C(C(C(C=COC4(C(c3c1O4)O)C)OC)C)OC(=O)C)C)O)C)O)C)C)O)O
OpenEye OEToolkits 1.7.6Cc1c(c2c3c(cc(c2O)NC(=O)C(=C/C=C/[C@@H]([C@@H]([C@H]([C@H]([C@H]([C@@H]([C@@H]([C@H](/C=C/O[C@@]4([C@@H](c3c1O4)O)C)OC)C)OC(=O)C)C)O)C)O)C)C)O)O
CACTVS 3.385CO[CH]1C=CO[C]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)C(=CC=C[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]1C)C)cc(O)c4c3[CH]2O
CACTVS 3.385CO[C@H]1/C=C/O[C@@]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)\C(=C/C=C/[C@H](C)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)C)cc(O)c4c3[C@H]2O
ACDLabs 12.01O=C(OC4C(C)C(OC)C=COC3(Oc2c(c(O)c1c(O)c(cc(O)c1c2C3O)NC(=O)C(=CC=CC(C)C(O)C(C)C(O)C4C)C)C)C)C
FormulaC37 H49 N O12
Namerifamycin SV
ChEMBL
DrugBank
ZINC
PDB chain4oir 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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PDB4oir GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.
Resolution3.105 Å
Binding residue
(original residue number in PDB)		Q390 Q393 F394 R405 R409 S411 L413 N448 I452
Binding residue
(residue number reindexed from 1)		Q384 Q387 F388 R399 R403 S405 L407 N442 I446
Annotation score1
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:4oir, PDBe:4oir, PDBj:4oir
PDBsum4oir
PubMed24755292
UniProtQ8RQE9|RPOB_THET8 DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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