Structure of PDB 6bed Chain C Binding Site BS01

Receptor Information
>6bed Chain C (length=530) Species: 10254 (Vaccinia virus WR) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKRSNVFAVDSQIPTLYMPQYISLSGVMTNDDNQAIASFEIRDQYITALN
HLVLSLELPEVKGMGRFGYVPYVGYKCINHVSISSCNGVIWEIEGEELYN
NCINNTIALKHSGYSSELNDISIGLTPNDTIKEPSTVYVYIKTPFDVEDT
FSSLKLSDSKITVTVTFNPVSDIVIRDSSFDFETFNKEFVYVPELSFIGY
MVKNVQIKPSFIEKPRRVIGQINQPTATVTEVHAATSLSVYTKPYYGNTD
NKFISYPGYSQDEKDYIDAYVSRLLDDLVIVSDGPPTGYPESAEIVEVPE
DGIVSIQDADVYVKIDNVPDNMSVYLHTNLLMFGTRKNSFIYNISKKFSA
ITGTYSDATKRTIFAHISHSINIIDTSIPVSLWTSQRNVYNGDNRSAESK
AKDLFINDPFIKGIDFKNKTDIISRLEVRFGNDVLYSENGPISRIYNELL
TKSNNGTRTLTFNFTPKIFFRPTTITANVSRGKDKLSVRVVYSTMDVNHP
IYYVQKQLVVVCNDLYKVSYDQGVSITKIM
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 chain6bed Chain C Residue 601 [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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PDB6bed Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.
Resolution2.75 Å
Binding residue
(original residue number in PDB)		Q27 F168 F486
Binding residue
(residue number reindexed from 1)		Q12 F151 F469
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.72,Kd=19uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0042802 identical protein binding
Biological Process
GO:0046677 response to antibiotic
Cellular Component
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6bed, PDBe:6bed, PDBj:6bed
PDBsum6bed
PubMed30068608
UniProtP68440|PG125_VACCW Scaffold protein OPG125 (Gene Name=OPG125)

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