Structure of PDB 6beh Chain B Binding Site BS01

Receptor Information
>6beh Chain B (length=544) Species: 10254 (Vaccinia virus WR) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAMNNTIINSLIGDSIKRSNVFAVDSQIPTLYMPQYISLSGVMTNDNQAI
ASFEIRDQYITALNHLVLSLELPEVKGMGRFGYVPYVGYKCINHVSISSC
NGVIWEIEGEELYNNCINNTIALKHSGYSSELNDISIGLTPNDTIKEPST
VYVYIKTPFDVEDTFSSLKLSDSKITVTVTFNPVSDIVIRDSSFDFETFN
KEFVYVPELSFIGYMVKNVQIKPSFIEKPRRVIGQINQPTATVTEVHAAT
SLSVYTKPYYGNTDNKFISYPGYSQDEKDYIDAYVSRLLDDLVIVSDGPP
TGYPESAEIVEVPEDGIVSIQDADVYVKIDNVPDNMSVYLHTNLLMFGTR
KNSFIYNISKKFSAITGTYSDATKRTIFAHISHSINIIDTSIPVSLWTSQ
RNVYNGDNRSAESKAKDLFINDPFIKGIDFKNKTDIISRLEVRFGNDVLY
SENGPISRIYNELLTKSNNGTRTLTFNFTPKIFFRPTTITANVSRGKDKL
SVRVVYSTMDVNHPIYYVQKQLVVVCNDLYKVSYDQGVSITKIM
Ligand information
Ligand IDRPT
InChIInChI=1S/C47H64N4O12/c1-24-13-12-14-25(2)46(59)49-37-32(23-48-51-20-18-50(19-21-51)31-15-10-11-16-31)41(56)34-35(42(37)57)40(55)29(6)44-36(34)45(58)47(8,63-44)61-22-17-33(60-9)26(3)43(62-30(7)52)28(5)39(54)27(4)38(24)53/h12-14,17,22-24,26-28,31,33,38-39,43,53-57H,10-11,15-16,18-21H2,1-9H3,(H,49,59)/b13-12+,22-17+,25-14-,48-23+/t24-,26+,27+,28+,33-,38-,39+,43+,47-/m0/s1
InChIKeyWDZCUPBHRAEYDL-GZAUEHORSA-N
SMILES
SoftwareSMILES
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(CC5)C6CCCC6)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)C6CCCC6)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
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)C6CCCC6)\C)C)O)C)O)C)OC(=O)C)C)OC)C)O
ACDLabs 10.04O=C5c6c3c(O)c(\C=N\N2CCN(C1CCCC1)CC2)c4c(O)c3c(O)c(c6OC5(OC=CC(OC)C(C(OC(=O)C)C(C)C(O)C(C)C(O)C(C=CC=C(C(=O)N4)C)C)C)C)C
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(CC5)C6CCCC6)c(O)c4c3C2=O
FormulaC47 H64 N4 O12
NameRIFAPENTINE;
(2R,16S,17R,18R,19R,20S,21S,22S,23S)-8-{[(4-CYCLOPENTYLPIPERAZIN-1-YL)IMINO]METHYL}-5,6,9,17,19-PENTAHYDROXY-23-METHOXY -2,4,12,16,18,20,22-HEPTAMETHYL-1,11-DIOXO-1,2-DIHYDRO-2,7-(EPOXYPENTADECA[1,11,13]TRIENOIMINO)NAPHTHO[2,1-B]FURAN-21-YL ACETATE;
3-(((4-CYCLOPENTYL-1-PIPERAZINYL)IMINO)METHYL)RIFAMYCIN
ChEMBLCHEMBL1660
DrugBankDB01201
ZINCZINC000169621228
PDB chain6beh 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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PDB6beh Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.
Resolution3.0 Å
Binding residue
(original residue number in PDB)
S19 F486
Binding residue
(residue number reindexed from 1)
S19 F483
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.09,Kd=82uM
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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:6beh, PDBe:6beh, PDBj:6beh
PDBsum6beh
PubMed30068608
UniProtP68440|PG125_VACCW Scaffold protein OPG125 (Gene Name=OPG125)

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