Structure of PDB 6beb Chain A Binding Site BS01

Receptor Information
>6beb Chain A (length=531) Species: 10254 (Vaccinia virus WR) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNIKRSNVFAVDSQIPTLYMPQYISLSGVMTNDNQAIASFEIRDQYITAL
NHLVLSLELPEVKGMGRFGYVPYVGYKCINHVSISSCNGVIWEIEGEELY
NNCINNTIALKHSGYSSELNDISIGLTPNDTIKEPSTVYVYIKTPFDVED
TFSSLKLSDSKITVTVTFNPVSDIVIRDSSFDFETFNKEFVYVPELSFIG
YMVKNVQIKPSFIEKPRRVIGQINQPTATVTEVHAATSLSVYTKPYYGNT
DNKFISYPGYSQDEKDYIDAYVSRLLDDLVIVSDGPPTGYPESAEIVEVP
EDGIVSIQDADVYVKIDNVPDNMSVYLHTNLLMFGTRKNSFIYNISKKFS
AITGTYSDATKRTIFAHISHSINIIDTSIPVSLWTSQRNVYNGDNRSAES
KAKDLFINDPFIKGIDFKNKTDIISRLEVRFGNDVLYSENGPISRIYNEL
LTKSNNGTRTLTFNFTPKIFFRPTTITANVSRGKDKLSVRVVYSTMGVNH
PIYYVQKQLVVVCNDLYKVSYDQGVSITKIM
Ligand information
Ligand IDRFV
InChIInChI=1S/C37H49NO12/c1-16-11-10-12-17(2)36(46)38-23-15-24(40)26-27(32(23)44)31(43)21(6)34-28(26)35(45)37(8,50-34)48-14-13-25(47-9)18(3)33(49-22(7)39)20(5)30(42)19(4)29(16)41/h10-16,18-20,25,29-30,33,35,40-45H,1-9H3,(H,38,46)/b11-10+,14-13+,17-12-/t16-,18+,19+,20+,25-,29-,30+,33+,35+,37-/m0/s1
InChIKeyOUOULRWGQDSKTQ-ZVFQNIRDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c(c2c3c(cc(c2O)NC(=O)C(=CC=CC(C(C(C(C(C(C(C(C=COC4(C(c3c1O4)O)C)OC)C)OC(=O)C)C)O)C)O)C)C)O)O
OpenEye OEToolkits 1.7.6Cc1c(c2c3c(cc(c2O)NC(=O)C(=C/C=C/[C@@H]([C@@H]([C@H]([C@H]([C@H]([C@@H]([C@@H]([C@H](/C=C/O[C@@]4([C@@H](c3c1O4)O)C)OC)C)OC(=O)C)C)O)C)O)C)C)O)O
CACTVS 3.385CO[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)cc(O)c4c3[CH]2O
CACTVS 3.385CO[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)cc(O)c4c3[C@H]2O
ACDLabs 12.01O=C(OC4C(C)C(OC)C=COC3(Oc2c(c(O)c1c(O)c(cc(O)c1c2C3O)NC(=O)C(=CC=CC(C)C(O)C(C)C(O)C4C)C)C)C)C
FormulaC37 H49 N O12
Namerifamycin SV
ChEMBL
DrugBank
ZINC
PDB chain6beb Chain A 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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PDB6beb Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		F486 F487
Binding residue
(residue number reindexed from 1)		F470 F471
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.61,Kd=246uM
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:6beb, PDBe:6beb, PDBj:6beb
PDBsum6beb
PubMed30068608
UniProtP68440|PG125_VACCW Scaffold protein OPG125 (Gene Name=OPG125)

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