Structure of PDB 6vvy Chain C Binding Site BS03

Receptor Information
>6vvy 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 IDSRN
InChIInChI=1S/C47H66O11/c1-30(17-14-15-23-44(50)51)27-31(2)47-40-26-25-34(54-47)18-10-6-5-7-11-19-35(48)46(53)43-28-36(49)32(3)37(56-43)21-16-22-38-33(4)41-29-42(55-38)39(57-41)20-12-8-9-13-24-45(52)58-40/h6,8-13,16,19-20,22,24-27,30,32-43,46-49,53H,5,7,14-15,17-18,21,23,28-29H2,1-4H3,(H,50,51)/b9-8-,10-6+,19-11+,20-12+,22-16+,24-13-,31-27+/t30-,32-,33+,34+,35+,36+,37-,38+,39-,40+,41-,42-,43-,46+,47+/m1/s1
InChIKeyOTABDKFPJQZJRD-QLGZCQHWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@H]1[C@H]2C\C=C\[C@H]3[C@@H]([C@H]4C[C@@H](O3)[C@H](O4)/C=C/C=C\C=C/C(=O)O[C@H]5C=C[C@H](C\C=C\CC\C=C\[C@@H]([C@@H]([C@H](O2)C[C@@H]1O)O)O)O[C@H]5/C(=C/[C@H](C)CCCCC(=O)O)/C)C
OpenEye OEToolkits 1.5.0CC1C2CC=CC3C(C4CC(O3)C(O4)C=CC=CC=CC(=O)OC5C=CC(CC=CCCC=CC(C(C(O2)CC1O)O)O)OC5C(=CC(C)CCCCC(=O)O)C)C
CACTVS 3.341C[CH](CCCCC(O)=O)C=C(C)[CH]1O[CH]2CC=CCCC=C[CH](O)[CH](O)[CH]3C[CH](O)[CH](C)[CH](CC=C[CH]4O[CH]5C[CH](O[CH]5C=CC=CC=CC(=O)O[CH]1C=C2)[CH]4C)O3
CACTVS 3.341C[C@H](CCCCC(O)=O)\C=C(/C)[C@@H]1O[C@H]2C\C=C\CC\C=C\[C@H](O)[C@H](O)[C@H]3C[C@H](O)[C@@H](C)[C@@H](C\C=C\[C@@H]4O[C@@H]5C[C@@H](O[C@@H]5\C=C\C=C/C=C\C(=O)O[C@H]1C=C2)[C@H]4C)O3
ACDLabs 10.04O=C2OC1C=CC(OC1C(=C/C(C)CCCCC(=O)O)/C)CC=CCCC=CC(O)C(O)C5OC(CC=CC4OC3CC(OC3C=CC=CC=C2)C4C)C(C)C(O)C5
FormulaC47 H66 O11
NameSORANGICIN A
ChEMBL
DrugBank
ZINCZINC000255256293
PDB chain6vvy 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6vvy The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase.
Resolution3.42 Å
Binding residue
(original residue number in PDB)		Q435 L436 Q438 F439 R454 S456 L458 P489
Binding residue
(residue number reindexed from 1)		Q406 L407 Q409 F410 R425 S427 L429 P460
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:6vvy, PDBe:6vvy, PDBj:6vvy
PDBsum6vvy
PubMed33199626
UniProtP9WGY9|RPOB_MYCTU DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

[Back to BioLiP]