Structure of PDB 6bec Chain A Binding Site BS01

Receptor Information
>6bec Chain A (length=540) Species: 10254 (Vaccinia virus WR) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMNNTIINSLSIKRSNVFAVDSQIPTLYMPQYISLSGVMTNDNQAIASFE
IRDQYITALNHLVLSLELPEVKGMGRFGYVPYVGYKCINHVSISSCNGVI
WEIEGEELYNNCINNTIALKHSGYSSELNDISIGLTPNDTIKEPSTVYVY
IKTPFDVEDTFSSLKLSDSKITVTVTFNPVSDIVIRDSSFDFETFNKEFV
YVPELSFIGYMVKNVQIKPSFIEKPRRVIGQINQPTATVTEVHAATSLSV
YTKPYYGNTDNKFISYPGYSQDEKDYIDAYVSRLLDDLVIVSDGPPTGYP
ESAEIVEVPEDGIVSIQDADVYVKIDNVPDNMSVYLHTNLLMFGTRKNSF
IYNISKKFSAITGTYSDATKRTIFAHISHSINIIDTSIPVSLWTSQRNVY
NGDNRSAESKAKDLFINDPFIKGIDFKNKTDIISRLEVRFGNDVLYSENG
PISRIYNELLTKSNNGTRTLTFNFTPKIFFRPTTITANVSRGKDKLSVRV
VYSTMDVNHPIYYVQKQLVVVCNDLYKVSYDQGVSITKIM
Ligand information
Ligand IDRBT
InChIInChI=1S/C46H62N4O11/c1-22(2)21-50-18-16-46(17-19-50)48-34-31-32-39(54)28(8)42-33(31)43(56)45(10,61-42)59-20-15-30(58-11)25(5)41(60-29(9)51)27(7)38(53)26(6)37(52)23(3)13-12-14-24(4)44(57)47-36(40(32)55)35(34)49-46/h12-15,20,22-23,25-27,30,37-38,41,49,52-54H,16-19,21H2,1-11H3,(H,47,57)/b13-12+,20-15+,24-14-/t23-,25+,26+,27+,30-,37-,38+,41+,45-/m0/s1
InChIKeyATEBXHFBFRCZMA-VXTBVIBXSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CO[CH]1C=CO[C]2(C)Oc3c(C)c(O)c4C(=O)C(=C5NC6(CCN(CC6)CC(C)C)N=C5c4c3C2=O)NC(=O)C(=CC=C[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]1C)C
CACTVS 3.341CO[C@H]1\C=C\O[C@@]2(C)Oc3c(C)c(O)c4C(=O)C(=C5NC6(CCN(CC6)CC(C)C)N=C5c4c3C2=O)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
ACDLabs 10.04O=C4c5c2C1=NC6(NC1=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)CCN(CC(C)C)CC6
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(=C5C3=NC6(N5)CCN(CC6)CC(C)C)C2=O)\C)C)O)C)O)C)OC(=O)C)C)OC)C)O
OpenEye OEToolkits 1.5.0Cc1c(c2c3c4c1OC(C4=O)(OC=CC(C(C(C(C(C(C(C(C=CC=C(C(=O)NC(=C5C3=NC6(N5)CCN(CC6)CC(C)C)C2=O)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
FormulaC46 H62 N4 O11
NameRIFABUTIN;
(9S,12E,14S,15R,16S,17R,18R,19R,20S,21S,22E,24Z)-6-16,18,20- TETRAHYDROXY-1'-ISOBUTYL-14-METHOXY-7,9,15,17,19,21,25- HEPTAMETHYLSPIRO(9,4-(EPOXYPENTADECA(1,11,13)TRIENIMINO)-2H- FURO(2',3':7,8)NAPHTH(1,2-D)IMIDAZOLE-2,4'-PIPERIDINE)- 5,10,26(3H,9H)-TRIONE,16-ACETATE;
ANSAMYCIN
ChEMBLCHEMBL444633
DrugBankDB00615
ZINCZINC000169621215
PDB chain6bec 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

[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]
PDB6bec Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.
Resolution2.91 Å
Binding residue
(original residue number in PDB)
P483 F486
Binding residue
(residue number reindexed from 1)
P476 F479
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.01,Kd=98uM
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:6bec, PDBe:6bec, PDBj:6bec
PDBsum6bec
PubMed30068608
UniProtP68440|PG125_VACCW Scaffold protein OPG125 (Gene Name=OPG125)

[Back to BioLiP]