Structure of PDB 6zdm Chain AAA Binding Site BS01

Receptor Information
>6zdm Chain AAA (length=383) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLL
DYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTF
KNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATRE
DFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDT
FAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSL
LFKKLVGTKVLMASVQGRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNV
TKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPP
LMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI
Ligand information
Ligand IDQG2
InChIInChI=1S/C22H27NO19S2/c1-7-4-12(24)39-10-5-8(2-3-9(7)10)38-22-17(28)16(27)18(19(42-22)20(29)30)41-21-13(23-43(31,32)33)15(26)14(25)11(40-21)6-37-44(34,35)36/h2-5,11,13-19,21-23,25-28H,6H2,1H3,(H,29,30)(H,31,32,33)(H,34,35,36)/t11-,13-,14-,15-,16-,17-,18+,19+,21-,22-/m1/s1
InChIKeyVWVHHIREMFENNG-XOAMEYKJSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1=CC(=O)Oc2cc(O[C@@H]3O[C@@H]([C@@H](O[C@H]4O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O)[C@H]4N[S](O)(=O)=O)[C@H](O)[C@H]3O)C(O)=O)ccc12
OpenEye OEToolkits 2.0.7CC1=CC(=O)Oc2c1ccc(c2)OC3C(C(C(C(O3)C(=O)O)OC4C(C(C(C(O4)COS(=O)(=O)O)O)O)NS(=O)(=O)O)O)O
CACTVS 3.385CC1=CC(=O)Oc2cc(O[CH]3O[CH]([CH](O[CH]4O[CH](CO[S](O)(=O)=O)[CH](O)[CH](O)[CH]4N[S](O)(=O)=O)[CH](O)[CH]3O)C(O)=O)ccc12
OpenEye OEToolkits 2.0.7CC1=CC(=O)Oc2c1ccc(c2)O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)C(=O)O)O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)COS(=O)(=O)O)O)O)NS(=O)(=O)O)O)O
FormulaC22 H27 N O19 S2
Name(2~{S},3~{S},4~{R},5~{R},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-4,5-bis(oxidanyl)-3-(sulfoamino)-6-(sulfooxymethyl)oxan-2-yl]oxy-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6zdm Chain AAA Residue 603 [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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PDB6zdm Structural insights into heparanase activity using a fluorogenic heparan sulfate disaccharide.
Resolution1.714 Å
Binding residue
(original residue number in PDB)
F160 N224 R273 Y298 E343 Y348 G349 G350 A388 G389 Y391
Binding residue
(residue number reindexed from 1)
F2 N66 R115 Y140 E185 Y190 G191 G192 A230 G231 Y233
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:6zdm, PDBe:6zdm, PDBj:6zdm
PDBsum6zdm
PubMed33073275
UniProtQ9Y251|HPSE_HUMAN Heparanase (Gene Name=HPSE)

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