Structure of PDB 8rdf Chain H Binding Site BS01

Receptor Information
>8rdf Chain H (length=222) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVQLVESGGGLVTPGGSLRLSCAASGFTFNTYSMNWVRQAPGKGLEWVSS
ISRSSDYIYYADSVKGRFTISRDNAKNSVYLQMTSLRDEDTAVYYCARDP
GGMPTTVTTWLYWGQGTLVTVSSASTKGPSVFPLAPSSTSGGTAALGCLV
KDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQ
TYICNVNHKPSNTKVDKRVEPK
Ligand information
Ligand IDA1H09
InChIInChI=1S/C30H59O34P3/c31-1-10(35)19(41)13(38)7-56-66(50,51)63-26-17(3-33)60-29(23(26)45)55-6-12(37)21(43)15(40)9-58-67(52,53)64-27-18(4-34)61-30(24(27)46)54-5-11(36)20(42)14(39)8-57-65(48,49)62-25-16(2-32)59-28(47)22(25)44/h10-47H,1-9H2,(H,48,49)(H,50,51)(H,52,53)/t10-,11-,12-,13+,14+,15+,16+,17+,18+,19-,20-,21-,22+,23+,24+,25+,26+,27+,28+,29+,30+/m0/s1
InChIKeyMUJPLVAWHMKDRT-KFDLCVIWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[C@H]1[C@@H](O)[C@H](OC[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[C@H]2[C@@H](O)[C@H](OC[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[C@H]3[C@@H](O)[C@H](O)O[C@@H]3CO)O[C@@H]2CO)O[C@@H]1CO
OpenEye OEToolkits 2.0.7C([C@@H]1[C@H]([C@H]([C@@H](O1)O)O)OP(=O)(O)OC[C@H]([C@H]([C@H](CO[C@H]2[C@@H]([C@@H]([C@H](O2)CO)OP(=O)(O)OC[C@H]([C@H]([C@H](CO[C@H]3[C@@H]([C@@H]([C@H](O3)CO)OP(=O)(O)OC[C@H]([C@H]([C@H](CO)O)O)O)O)O)O)O)O)O)O)O)O
CACTVS 3.385OC[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[CH]1[CH](O)[CH](OC[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[CH]2[CH](O)[CH](OC[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[CH]3[CH](O)[CH](O)O[CH]3CO)O[CH]2CO)O[CH]1CO
OpenEye OEToolkits 2.0.7C(C1C(C(C(O1)O)O)OP(=O)(O)OCC(C(C(COC2C(C(C(O2)CO)OP(=O)(O)OCC(C(C(COC3C(C(C(O3)CO)OP(=O)(O)OCC(C(C(CO)O)O)O)O)O)O)O)O)O)O)O)O
FormulaC30 H59 O34 P3
NameHaemophilus influenzae type b (Hib) DP3 oligosaccharide ;
[(2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)-4,5-bis(oxidanyl)oxolan-3-yl] [(2~{R},3~{S},4~{S})-5-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-4-[[(2~{R},3~{S},4~{S})-5-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3-oxidanyl-4-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentoxy]phosphoryl]oxy-oxolan-2-yl]oxy-2,3,4-tris(oxidanyl)pentoxy]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]oxy-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain8rdf Chain H Residue 301 [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]
PDB8rdf A Multidisciplinary Structural Approach to the Identification of the Haemophilus influenzae Type b Capsular Polysaccharide Protective Epitope
Resolution2.74 Å
Binding residue
(original residue number in PDB)
F27 T28 T31 Y32 S33 S52 R53 Y57 D99 G101 G102 M103 P104 T105 T106
Binding residue
(residue number reindexed from 1)
F27 T28 T31 Y32 S33 S52 R53 Y57 D99 G101 G102 M103 P104 T105 T106
Annotation score1
External links