Structure of PDB 8i8r Chain C Binding Site BS02

Receptor Information
>8i8r Chain C (length=345) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLT
GYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVT
SWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQG
KNGNPSGEGFTSGVTNNGRDALRQNGDGVGGSITYDYEGFGIGGAISSSK
RTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLG
WANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDVG
ATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF
Ligand information
Ligand IDKDL
InChIInChI=1S/C110H202N2O39P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-92(123)142-82(66-60-54-48-42-35-29-23-17-11-5)72-94(125)146-104-96(112-90(121)71-81(65-59-53-47-41-34-28-22-16-10-4)141-91(122)67-61-55-49-43-36-30-24-18-12-6)105(144-88(102(104)150-152(133,134)135)78-140-109(107(129)130)74-86(98(127)101(148-109)85(119)76-114)147-110(108(131)132)73-83(117)97(126)100(149-110)84(118)75-113)139-77-87-99(128)103(145-93(124)70-80(116)64-58-52-46-40-33-27-21-15-9-3)95(106(143-87)151-153(136,137)138)111-89(120)69-79(115)63-57-51-45-39-32-26-20-14-8-2/h79-88,95-106,113-119,126-128H,7-78H2,1-6H3,(H,111,120)(H,112,121)(H,129,130)(H,131,132)(H2,133,134,135)(H2,136,137,138)/t79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,109-,110-/m1/s1
InChIKeyDIXUKJUHGLIZGU-OIPVZEHTSA-N
SMILES
SoftwareSMILES
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](O3)[CH](O)CO)C(O)=O)[CH]1O[P](O)(O)=O
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCC(=O)OC(CCCCCCCCCCC)CC(=O)OC1C(C(OC(C1OP(=O)(O)O)COC2(CC(C(C(O2)C(CO)O)O)OC3(CC(C(C(O3)C(CO)O)O)O)C(=O)O)C(=O)O)OCC4C(C(C(C(O4)OP(=O)(O)O)NC(=O)CC(CCCCCCCCCCC)O)OC(=O)CC(CCCCCCCCCCC)O)O)NC(=O)CC(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCC(=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)O[C@@]3(C[C@H]([C@H]([C@H](O3)[C@@H](CO)O)O)O)C(=O)O)C(=O)O)OC[C@@H]4[C@H]([C@@H]([C@H]([C@H](O4)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](O3)[C@H](O)CO)C(O)=O)[C@H]1O[P](O)(O)=O
FormulaC110 H202 N2 O39 P2
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]-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]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain8i8r Chain C Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8i8r Molecular mechanism of phospholipid transport at the bacterial outer membrane interface
Resolution2.93 Å
Binding residue
(original residue number in PDB)
F109 Y111 Y170 K173 D199 V201 K222 R238
Binding residue
(residue number reindexed from 1)
F87 Y89 Y148 K151 D177 V179 K200 R216
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001618 virus receptor activity
GO:0005515 protein binding
GO:0015288 porin activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006811 monoatomic ion transport
GO:0006974 DNA damage response
GO:0034220 monoatomic ion transmembrane transport
GO:0046718 symbiont entry into host cell
GO:0046813 receptor-mediated virion attachment to host cell
GO:0120010 intermembrane phospholipid transfer
Cellular Component
GO:0009279 cell outer membrane
GO:0016020 membrane
GO:0046930 pore complex

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Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8i8r, PDBe:8i8r, PDBj:8i8r
PDBsum8i8r
PubMed38092770
UniProtP06996|OMPC_ECOLI Outer membrane porin C (Gene Name=ompC)

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