Structure of PDB 8frm Chain F Binding Site BS01

Receptor Information
>8frm 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 IDJSG
InChIInChI=1S/C131H240N2O63P4/c1-7-13-19-25-31-37-38-44-50-56-62-68-98(149)180-85(66-60-54-48-42-35-29-23-17-11-5)72-100(151)184-119-102(133-96(147)71-84(65-59-53-47-41-34-28-22-16-10-4)179-97(148)67-61-55-49-43-36-30-24-18-12-6)123(177-80-93-104(153)118(183-99(150)70-83(139)64-58-52-46-40-33-27-21-15-9-3)101(124(181-93)196-200(173,174)175)132-95(146)69-82(138)63-57-51-45-39-32-26-20-14-8-2)182-94(117(119)193-197(164,165)166)81-178-130(128(160)161)74-92(190-131(129(162)163)73-86(140)103(152)112(191-131)88(142)76-135)116(115(192-130)90(144)78-137)188-127-110(159)120(122(195-199(170,171)172)113(186-127)89(143)77-136)189-126-109(158)107(156)121(194-198(167,168)169)114(187-126)91(145)79-176-125-108(157)105(154)106(155)111(185-125)87(141)75-134/h82-94,101-127,134-145,152-159H,7-81H2,1-6H3,(H,132,146)(H,133,147)(H,160,161)(H,162,163)(H2,164,165,166)(H2,167,168,169)(H2,170,171,172)(H2,173,174,175)/t82-,83-,84-,85-,86-,87+,88-,89+,90-,91+,92-,93-,94-,101-,102-,103-,104-,105+,106+,107-,108+,109+,110+,111-,112-,113-,114-,115-,116-,117-,118-,119-,120-,121+,122-,123-,124-,125+,126-,127-,130-,131-/m1/s1
InChIKeyMVYTXVAKEAWEGM-SMTLFHDCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@@H]1[C@H]([C@@H](O[C@@H]([C@H]1OP(=O)(O)O)CO[C@@]2(C[C@H]([C@H]([C@H](O2)[C@@H](CO)O)O[C@@H]3[C@H]([C@H]([C@@H]([C@H](O3)[C@H](CO)O)OP(=O)(O)O)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)[C@H](CO[C@@H]5[C@H]([C@H]([C@@H]([C@H](O5)[C@H](CO)O)O)O)O)O)OP(=O)(O)O)O)O)O)O[C@@]6(C[C@H]([C@H]([C@H](O6)[C@@H](CO)O)O)O)C(=O)O)C(=O)O)OC[C@@H]7[C@H]([C@@H]([C@H]([C@H](O7)OP(=O)(O)O)NC(=O)C[C@@H](CCCCCCCCCCC)O)OC(=O)C[C@@H](CCCCCCCCCCC)O)O)NC(=O)C[C@@H](CCCCCCCCCCC)OC(=O)CCCCCCCCCCC
CACTVS 3.385CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@@H]1[C@@H](NC(=O)C[C@@H](CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)[C@H](OC[C@H]2O[C@H](O[P](O)(O)=O)[C@H](NC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H](OC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H]2O)O[C@H](CO[C@@]3(C[C@@H](O[C@@]4(C[C@@H](O)[C@@H](O)[C@H](O4)[C@H](O)CO)C(O)=O)[C@@H](O[C@H]5O[C@H]([C@@H](O)CO)[C@@H](O[P](O)(O)=O)[C@H](O[C@H]6O[C@H]([C@@H](O)CO[C@H]7O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@@H]7O)[C@@H](O[P](O)(O)=O)[C@H](O)[C@@H]6O)[C@@H]5O)[C@H](O3)[C@H](O)CO)C(O)=O)[C@H]1O[P](O)(O)=O
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCC(=O)OC(CCCCCCCCCCC)CC(=O)OC1C(C(OC(C1OP(=O)(O)O)COC2(CC(C(C(O2)C(CO)O)OC3C(C(C(C(O3)C(CO)O)OP(=O)(O)O)OC4C(C(C(C(O4)C(COC5C(C(C(C(O5)C(CO)O)O)O)O)O)OP(=O)(O)O)O)O)O)OC6(CC(C(C(O6)C(CO)O)O)O)C(=O)O)C(=O)O)OCC7C(C(C(C(O7)OP(=O)(O)O)NC(=O)CC(CCCCCCCCCCC)O)OC(=O)CC(CCCCCCCCCCC)O)O)NC(=O)CC(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC
CACTVS 3.385CCCCCCCCCCCCCC(=O)O[CH](CCCCCCCCCCC)CC(=O)O[CH]1[CH](NC(=O)C[CH](CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)[CH](OC[CH]2O[CH](O[P](O)(O)=O)[CH](NC(=O)C[CH](O)CCCCCCCCCCC)[CH](OC(=O)C[CH](O)CCCCCCCCCCC)[CH]2O)O[CH](CO[C]3(C[CH](O[C]4(C[CH](O)[CH](O)[CH](O4)[CH](O)CO)C(O)=O)[CH](O[CH]5O[CH]([CH](O)CO)[CH](O[P](O)(O)=O)[CH](O[CH]6O[CH]([CH](O)CO[CH]7O[CH]([CH](O)CO)[CH](O)[CH](O)[CH]7O)[CH](O[P](O)(O)=O)[CH](O)[CH]6O)[CH]5O)[CH](O3)[CH](O)CO)C(O)=O)[CH]1O[P](O)(O)=O
FormulaC131 H240 N2 O63 P4
Name(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain8frm 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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PDB8frm A new antibiotic traps lipopolysaccharide in its intermembrane transporter
Resolution3.14 Å
Binding residue
(original residue number in PDB)
I25 M26 R30 R55 E58 F59 T61 L62 W271 A310 I313 L316 I317
Binding residue
(residue number reindexed from 1)
I24 M25 R29 R54 E57 F58 T60 L61 W237 A276 I279 L282 I283
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:8frm, PDBe:8frm, PDBj:8frm
PDBsum8frm
PubMed38172635
UniProtQ6FFD7

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