Structure of PDB 8e08 Chain A Binding Site BS01

Receptor Information
>8e08 Chain A (length=385) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KFKNSTYSRSSVDVLYTFAKCSGLDLIFGLNALLRTSDGQWNSSNAQLLL
DYCASKGYNIDWELGNEPNSFRKKAGIFINGSQLGKDFIHLHKLLRKSTF
KNAKLYGPDVGQPRGKTAKMLKSFLKAGGEVIDAVTWHHYYLNGRTATLE
DFLNPDVLDTFISQVQKVLQVVESTRPGKKVWLGETSSAYGGGAPGLSDT
FAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSL
LFKKLVGTKVLMASVQGQDRRKLRVYLHCTNTDNPRYKEGDLTLYAINLH
NVTKYLRLPYPFSNKQVDQYLLRPHGPDGLLSKSVQLNGQTLKMVDDQTL
PPLKPKPLRPGSSLGLPAFSYAFFVIRNAKVPACI
Ligand information
Ligand IDXY6
InChIInChI=1S/C5H10O11S2/c6-2-1-14-5(7)4(16-18(11,12)13)3(2)15-17(8,9)10/h2-7H,1H2,(H,8,9,10)(H,11,12,13)/t2-,3+,4-,5-/m1/s1
InChIKeyPCTZUCFLPZUYKQ-KKQCNMDGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C1[C@H]([C@@H]([C@H]([C@@H](O1)O)OS(=O)(=O)O)OS(=O)(=O)O)O
OpenEye OEToolkits 2.0.7C1C(C(C(C(O1)O)OS(=O)(=O)O)OS(=O)(=O)O)O
CACTVS 3.385O[C@@H]1CO[C@@H](O)[C@H](O[S](O)(=O)=O)[C@H]1O[S](O)(=O)=O
CACTVS 3.385O[CH]1CO[CH](O)[CH](O[S](O)(=O)=O)[CH]1O[S](O)(=O)=O
ACDLabs 12.01OC1OCC(O)C(OS(=O)(=O)O)C1OS(=O)(=O)O
FormulaC5 H10 O11 S2
Name2,3-di-O-sulfo-beta-D-xylopyranose
ChEMBL
DrugBank
ZINC
PDB chain8e08 Chain C Residue 2 [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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PDB8e08 Complex Inhibitory Mechanism of Glycomimetics with Heparanase.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		G273 K274
Binding residue
(residue number reindexed from 1)		G115 K116
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.166: heparanase.
Gene Ontology
Molecular Function
GO:0016798 hydrolase activity, acting on glycosyl bonds
Cellular Component
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:8e08, PDBe:8e08, PDBj:8e08
PDBsum8e08
PubMed37368361
UniProtQ9Y251|HPSE_HUMAN Heparanase (Gene Name=HPSE)

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