Structure of PDB 2ybu Chain E Binding Site BS01

Receptor Information
>2ybu Chain E (length=376) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AYQLTCYFTNWAQYRPGLGRFMPDDINPCLCTHLIYAFAGMQNNEITTIE
WNDVTLYQAFNGLKNKNSQLKTLLAIGGWNFGTAPFTAMVSTPENRQTFI
TSVIKFLRQYEFDGLDFDWEYPGSRGSPPQDKHLFTVLVQEMREAFEQEA
KQINKPRLMVTAAVAAGISNIQSGYEIPQLSQYLDYIHVMTYDLHGSWEG
YTGENSPLYKYPTDTGSNAYLNVDYVMNYWKDNGAPAEKLIVGFPTYGHN
FILSNPSNTGIGAPTSGAGPAGPYAKESGIWAYYEICTFLKNGATQGWDA
PQEVPYAYQGNVWVGYDNIKSFDIKAQWLKHNKFGGAMVWAIDLDDFTGT
FCNQGKFPLISTLKKALGLQSASCTA
Ligand information
Ligand IDCX9
InChIInChI=1S/C16H18N8O4/c1-20-8-19-12-10(20)14(26)24(16(28)22(12)3)6-4-5-23-13(25)9-11(18-7-17-9)21(2)15(23)27/h7-8H,4-6H2,1-3H3,(H,17,18)
InChIKeyPUHJHZQYIBJCSQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1Cn1cnc2c1C(=O)N(C(=O)N2C)CCCN3C(=O)c4c([nH]cn4)N(C3=O)C
CACTVS 3.352Cn1cnc2N(C)C(=O)N(CCCN3C(=O)N(C)c4[nH]cnc4C3=O)C(=O)c12
FormulaC16 H18 N8 O4
Name3,7-DIMETHYL-1-[3-(3-METHYL-2,6-DIOXO-9H-PURIN-1-YL)PROPYL]PURINE-2,6-DIONE;
BISDIONIN F;
3,7-DIMETHYL-1-[3-(3-METHYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-1-YL)PROPYL]-2,3,6,7-TETRAHYDRO-1H-PURINE-2,6-DIONE
ChEMBLCHEMBL1738785
DrugBank
ZINCZINC000034602313
PDB chain2ybu Chain E Residue 1398 [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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PDB2ybu Analyzing airway inflammation with chemical biology: dissection of acidic mammalian chitinase function with a selective drug-like inhibitor.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		W31 F58 G98 N100 D138 M210 Y212 W360
Binding residue
(residue number reindexed from 1)		W11 F38 G78 N80 D118 M190 Y192 W340
Annotation score1
Binding affinityMOAD: Ki=0.42uM
BindingDB: IC50=920nM
Enzymatic activity
Catalytic site (original residue number in PDB) D136 D138 E140 Y212
Catalytic site (residue number reindexed from 1) D116 D118 E120 Y192
Enzyme Commision number 3.2.1.14: chitinase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0008061 chitin binding
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2ybu, PDBe:2ybu, PDBj:2ybu
PDBsum2ybu
PubMed21609838
UniProtQ9BZP6|CHIA_HUMAN Acidic mammalian chitinase (Gene Name=CHIA)

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