Structure of PDB 8frl Chain F Binding Site BS01

Receptor Information
>8frl Chain F (length=316) Species: 62977 (Acinetobacter baylyi ADP1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IIRRYLVKQVVSTSLVVIALLTLIMMGGRLIKYFGVAAQGRLDAGVLFSI
IGYRMPEFLTLILPLGFFIGLMLVFGRLYVDHEMAVLNGSGISRIRLGQL
LIPLALVFLVIQGILMLWMTPWGLRQFDQLSSSQAVRTGFDLVRPKEFIS
SGPYTIYAGDLSEDRKNLKDIFFYQDVMILAKEATRNVVDLIQGRRYEIY
SQAEFQRYRLRLKVEALPSSKLWNKWNDPVIASEMGWRVFGPFTIVIALM
MAVALCEVSPRQGRYYRLIPAIFIFASLIVLLIAIRTRISRDELGVWAYP
AALAVYGIAAALFSRK
Ligand information
Ligand IDY75
InChIInChI=1S/C41H49ClN10O3S/c1-52-35(20-27-23-47-32-10-3-2-9-29(27)32)39(54)50-24-30-28(25-13-16-36(45)49-21-25)14-15-31(42)37(30)56-40-26(8-7-19-46-40)22-48-33(12-6-18-44)38(53)51-34(41(52)55)11-4-5-17-43/h2-3,7-10,13-16,19,21,23,33-35,47-48H,4-6,11-12,17-18,20,22,24,43-44H2,1H3,(H2,45,49)(H,50,54)(H,51,53)/t33-,34-,35-/m0/s1
InChIKeyBDHOZQIIBFIAMB-IMKBVMFZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Nc1ccc(cn1)c1ccc(Cl)c2Sc3ncccc3CNC(CCCN)C(=O)NC(CCCCN)C(=O)N(C)C(Cc3c[NH]c4ccccc43)C(=O)NCc12
CACTVS 3.385CN1[CH](Cc2c[nH]c3ccccc23)C(=O)NCc4c(Sc5ncccc5CN[CH](CCCN)C(=O)N[CH](CCCCN)C1=O)c(Cl)ccc4c6ccc(N)nc6
CACTVS 3.385CN1[C@@H](Cc2c[nH]c3ccccc23)C(=O)NCc4c(Sc5ncccc5CN[C@@H](CCCN)C(=O)N[C@@H](CCCCN)C1=O)c(Cl)ccc4c6ccc(N)nc6
OpenEye OEToolkits 2.0.7CN1C(C(=O)NCc2c(ccc(c2Sc3c(cccn3)CNC(C(=O)NC(C1=O)CCCCN)CCCN)Cl)c4ccc(nc4)N)Cc5c[nH]c6c5cccc6
OpenEye OEToolkits 2.0.7CN1[C@H](C(=O)NCc2c(ccc(c2Sc3c(cccn3)CN[C@H](C(=O)N[C@H](C1=O)CCCCN)CCCN)Cl)c4ccc(nc4)N)Cc5c[nH]c6c5cccc6
FormulaC41 H49 Cl N10 O3 S
Name(7S,10S,13S,17P)-10-(4-aminobutyl)-7-(3-aminopropyl)-17-(6-aminopyridin-3-yl)-20-chloro-13-[(1H-indol-3-yl)methyl]-12-methyl-6,7,9,10,12,13,15,16-octahydropyrido[2,3-b][1,5,8,11,14]benzothiatetraazacycloheptadecine-8,11,14(5H)-trione
ChEMBL
DrugBank
ZINC
PDB chain8frl Chain F Residue 401 [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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PDB8frl A new antibiotic traps lipopolysaccharide in its intermembrane transporter
Resolution3.2 Å
Binding residue
(original residue number in PDB)
E58 W271 I317 R320 T321
Binding residue
(residue number reindexed from 1)
E57 W237 I283 R286 T287
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0015920 lipopolysaccharide transport
GO:0055085 transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0043190 ATP-binding cassette (ABC) transporter complex

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8frl, PDBe:8frl, PDBj:8frl
PDBsum8frl
PubMed38172635
UniProtQ6FFD7

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