Structure of PDB 5uh6 Chain C Binding Site BS03

Receptor Information
>5uh6 Chain C (length=1126) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAER
GDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDM
TYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVS
QLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRID
RKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDI
YRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEP
ITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRR
LRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAI
KEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHP
SHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDE
IVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVD
YMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVG
TGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFAR
SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWE
GHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNIS
DEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGE
KAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKR
KISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMN
IGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVF
DGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGY
MYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQ
AYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKE
LQSLCLNVEVLSSDGAAIELREGEDE
Ligand information
Ligand IDRFP
InChIInChI=1S/C43H58N4O12/c1-21-12-11-13-22(2)42(55)45-33-28(20-44-47-17-15-46(9)16-18-47)37(52)30-31(38(33)53)36(51)26(6)40-32(30)41(54)43(8,59-40)57-19-14-29(56-10)23(3)39(58-27(7)48)25(5)35(50)24(4)34(21)49/h11-14,19-21,23-25,29,34-35,39,49-53H,15-18H2,1-10H3,(H,45,55)/b12-11+,19-14+,22-13-,44-20+/t21-,23+,24+,25+,29-,34-,35+,39+,43-/m0/s1
InChIKeyJQXXHWHPUNPDRT-WLSIYKJHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](C=C\C=C(/C(=O)Nc(c2O)c(c3O)\C=N\N5CCN(CC5)C)\C)C)O)C)O)C)OC(=O)C)C)OC)C)O
ACDLabs 10.04O=C4c5c2c(O)c(\C=N\N1CCN(C)CC1)c3c(O)c2c(O)c(c5OC4(OC=CC(OC)C(C(OC(=O)C)C(C)C(O)C(C)C(O)C(C=CC=C(C(=O)N3)C)C)C)C)C
CACTVS 3.341CO[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)c(C=NN5CCN(C)CC5)c(O)c4c3C2=O
CACTVS 3.341CO[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)c(\C=N\N5CCN(C)CC5)c(O)c4c3C2=O
OpenEye OEToolkits 1.5.0Cc1c(c2c3c4c1OC(C4=O)(OC=CC(C(C(C(C(C(C(C(C=CC=C(C(=O)Nc(c2O)c(c3O)C=NN5CCN(CC5)C)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
FormulaC43 H58 N4 O12
NameRIFAMPICIN
ChEMBLCHEMBL374478
DrugBankDB01045
ZINCZINC000169621223
PDB chain5uh6 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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PDB5uh6 Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition.
Resolution3.837 Å
Binding residue
(original residue number in PDB)		Q435 Q438 F439 H451 R454 S456 L458 N493 I497 R613 H680
Binding residue
(residue number reindexed from 1)		Q408 Q411 F412 H424 R427 S429 L431 N466 I470 R586 H653
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:5uh6, PDBe:5uh6, PDBj:5uh6
PDBsum5uh6
PubMed28392175
UniProtP9WGY9|RPOB_MYCTU DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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