Structure of PDB 6bzo Chain C Binding Site BS01

Receptor Information
>6bzo Chain C (length=1111) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGD
VNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTY
AAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQL
VRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRK
RRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYR
KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPIT
SSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLR
TVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE
FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSH
YGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIV
YLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYM
DVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTG
MELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSN
HGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGH
NYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDE
VLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKA
REVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKI
SDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIG
QILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDG
AQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMY
IMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAY
GAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQ
SLCLNVEVLSS
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)		M1051 I1052 Q1054 D1094 T1096 E1119 S1120
Binding residue
(residue number reindexed from 1)		M1022 I1023 Q1025 D1065 T1067 E1090 S1091
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:0005515 protein binding
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0006351 DNA-templated transcription
GO:0046677 response to antibiotic
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
UniProtP9WGY9|RPOB_MYCTU DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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