Structure of PDB 6bzo Chain D Binding Site BS01

Receptor Information
>6bzo Chain D (length=1263) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFG
PTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTH
IWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEA
EMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGGER
EMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEYFT
GAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAAFQ
QSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNR
LKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLS
DLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFK
PFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPT
LHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQA
EARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQPAS
GDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELFGH
SGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAER
YPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEERA
DKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIITIV
DSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINT
HGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVELAE
RAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALL
AAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSI
GEPGTQLTMITGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKI
TIVPDDGGEEVVYDKISKRQRLRVFKERVLSDGDHVEVGQQLMEGSADPH
EVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIID
SGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASLATDS
WLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRN
IAVQPTEEARAAA
Ligand information
Ligand IDFI8
InChIInChI=1S/C52H74Cl2O18/c1-13-30-22-26(6)33(56)18-16-15-17-31(23-66-51-45(65-12)42(61)44(29(9)67-51)69-49(64)35-32(14-2)36(53)39(58)37(54)38(35)57)48(63)68-34(28(8)55)20-19-25(5)21-27(7)43(30)70-50-41(60)40(59)46(52(10,11)72-50)71-47(62)24(3)4/h15-17,19,21-22,24,28-30,33-34,40-46,50-51,55-61H,13-14,18,20,23H2,1-12H3/b16-15+,25-19+,26-22+,27-21+,31-17+/t28-,29-,30+,33+,34+,40-,41+,42+,43+,44-,45+,46+,50-,51-/m1/s1
InChIKeyZVGNESXIJDCBKN-UUEYKCAUSA-N
SMILES
SoftwareSMILES
CCc1c(c(c(c(c1Cl)O)Cl)O)C(=O)O[C@@H]2[C@H](O[C@H]([C@H]([C@H]2O)OC)OC/C/3=C\C=C\C[C@@H](/C(=C/[C@@H]([C@H](/C(=C/C(=C/C[C@H](OC3=O)[C@@H](C)O)/C)/C)O[C@H]4[C@H]([C@H]([C@@H](C(O4)(C)C)OC(=O)C(C)C)O)O)CC)/C)O)C
CC[C@H]1\C=C(/C)[C@@H](O)C\C=C\C=C(/CO[C@@H]2O[C@H](C)[C@@H](OC(=O)c3c(O)c(Cl)c(O)c(Cl)c3CC)[C@H](O)[C@@H]2OC)C(=O)O[C@@H](C/C=C(C)/C=C(C)/[C@@H]1O[C@@H]4OC(C)(C)[C@@H](OC(=O)C(C)C)[C@H](O)[C@@H]4O)[C@@H](C)O
OpenEye OEToolkits 2.0.6CCc1c(c(c(c(c1Cl)O)Cl)O)C(=O)OC2C(OC(C(C2O)OC)OCC3=CC=CCC(C(=CC(C(C(=CC(=CCC(OC3=O)C(C)O)C)C)OC4C(C(C(C(O4)(C)C)OC(=O)C(C)C)O)O)CC)C)O)C
CACTVS 3.385CC[CH]1C=C(C)[CH](O)CC=CC=C(CO[CH]2O[CH](C)[CH](OC(=O)c3c(O)c(Cl)c(O)c(Cl)c3CC)[CH](O)[CH]2OC)C(=O)O[CH](CC=C(C)C=C(C)[CH]1O[CH]4OC(C)(C)[CH](OC(=O)C(C)C)[CH](O)[CH]4O)[CH](C)O
FormulaC52 H74 Cl2 O18
NameFidaxomicin
ChEMBLCHEMBL1255800
DrugBankDB08874
ZINC
PDB chain6bzo Chain C Residue 1201 [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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PDB6bzo Fidaxomicin jamsMycobacterium tuberculosisRNA polymerase motions needed for initiation via RbpA contacts.
Resolution3.38 Å
Binding residue
(original residue number in PDB)		R89 E323 S338 R412
Binding residue
(residue number reindexed from 1)		R86 E320 S335 R409
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: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
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6bzo, PDBe:6bzo, PDBj:6bzo
PDBsum6bzo
PubMed29480804
UniProtP9WGY7|RPOC_MYCTU DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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