Structure of PDB 8frl Chain G Binding Site BS01

Receptor Information
>8frl Chain G (length=338) Species: 62977 (Acinetobacter baylyi ADP1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RRIVAKHVTKTTALAMLGTTIVLVILQVLFTYLGELSNLKADYSAWQAFL
YVLWGAPRYLYEILPISALIGAILGLGTLASNSELIVMRSVGISLWRIVG
WVIRSALVLVLLSFALSEWVVPYTNERANSVKSHEVRGYWSREGQRFIYV
DYANSQGQLKRIQVVDFDDNYRLKSVTNAEQGQFVKDGQWLLNHSQQMAI
LANAAKQPFSLALQPKYVHMVTIDPEDLSFSQLVSFMNYMREYSQVPKTY
QLAFWKKVASPFALITLVLVACSFIFGPLRQQSMGFRLVIALFIGLGFYY
LQDFLGYASLVYNPSPAWFVLGPIVLMFVAGSYLLYRA
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 chain8frl Chain F Residue 402 [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)
F33 T34 E65 L309 F310 L313 Y316 Y317
Binding residue
(residue number reindexed from 1)
F30 T31 E62 L292 F293 L296 Y299 Y300
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
UniProtQ6FFD6

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