Structure of PDB 5yyb Chain A Binding Site BS01

Receptor Information
>5yyb Chain A (length=482) Species: 233412 ([Haemophilus] ducreyi 35000HP) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSTIEAGIAYPISTGFDPLTSSGASSMAANLHIFEGLVDLHPVTRQPYLA
LAAKEPEQKDDLTYYISLREGAMFHDGSPVTTEDVVYSFERVLDPAKASL
FAQFIPFIASVTALDDNVVEFKLKYPFALFKERLTIIKIVPKHIVEAGQS
AFDAKPIGSGPYKFVSATKDDRIVFEANTVYNGHYPAKVEKMTWFLLSDD
AARVTAQESGRVQAIESVPYLDAERLKRKNNVESVQSFGLLFLMFNCEKA
PFDNPKVRQALHYALDKQKLIDIVFLGNAKAATSYLQDTHPDYVKASSQY
DYDKAKAEKLLAEAGITNLTFQLLATDHAWVKECAPLILESWNALSVVKV
TLQHLQSGALYSAHVDKGAYEVVIAPGDPSVFGNDLDLLLSWWYRGDVWP
KRRFRWANTAEYHEVQKLLDEAIKNPAGSKVAWQKAINIIAEQVPLYPII
HRKLPTAWNTKKLTDFQPLPTTGLSFLGVGRT
Ligand information
Ligand IDNGE
InChIInChI=1S/C11H19NO10/c13-2-5(16)8(18)9-7(12-6(17)3-14)4(15)1-11(21,22-9)10(19)20/h4-5,7-9,13-16,18,21H,1-3H2,(H,12,17)(H,19,20)/t4-,5+,7+,8+,9+,11-/m0/s1
InChIKeyFDJKUWYYUZCUJX-AJKRCSPLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1C1[C@@H]([C@H]([C@@H](O[C@@]1(C(=O)O)O)[C@@H]([C@@H](CO)O)O)NC(=O)CO)O
CACTVS 3.352OC[C@@H](O)[C@@H](O)[C@@H]1O[C@@](O)(C[C@H](O)[C@H]1NC(=O)CO)C(O)=O
OpenEye OEToolkits 1.6.1C1C(C(C(OC1(C(=O)O)O)C(C(CO)O)O)NC(=O)CO)O
CACTVS 3.352OC[CH](O)[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1NC(=O)CO)C(O)=O
ACDLabs 10.04O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)CO)C(O)C1
FormulaC11 H19 N O10
NameN-glycolyl-beta-neuraminic acid;
N-glycolylneuraminic acid;
sialic acid
ChEMBLCHEMBL496421
DrugBank
ZINCZINC000004096097
PDB chain5yyb Chain A Residue 501 [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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PDB5yyb Molecular characterization of the interaction of sialic acid with the periplasmic binding protein fromHaemophilus ducreyi.
Resolution2.484 Å
Binding residue
(original residue number in PDB)		S27 H333 S362 Y366 D383 P384 F387 W397 R408
Binding residue
(residue number reindexed from 1)		S22 H328 S357 Y361 D378 P379 F382 W392 R403
Annotation score4
Binding affinityMOAD: Kd=277nM
PDBbind-CN: -logKd/Ki=6.56,Kd=277nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:1904680 peptide transmembrane transporter activity
Biological Process
GO:0015833 peptide transport
GO:0055085 transmembrane transport
Cellular Component
GO:0030288 outer membrane-bounded periplasmic space
GO:0043190 ATP-binding cassette (ABC) transporter complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yyb, PDBe:5yyb, PDBj:5yyb
PDBsum5yyb
PubMed30315109
UniProtQ7VL18

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