Structure of PDB 1x38 Chain A Binding Site BS02

Receptor Information

>1x38 Chain A (length=602) Species: 4513 (Hordeum vulgare)

DYVLYKDATKPVEDRVADLLGRMTLAEKIGQMTQIERLVATPDVLRDNFI
GSLLSGGGSVPRKGATAKEWQDMVDGFQKACMSTRLGIPMIYGIDAVHGQ
NNVYGATIFPHNVGLGATRDPYLVKRIGEATALEVRATGIQYAFAPCIAV
CRDPRWGRCYESYSEDRRIVQSMTELIPGLQGDVPKDFTSGMPFVAGKNK
VAACAKHFVGDGGTVDGINENNTIINREGLMNIHMPAYKNAMDKGVSTVM
ISYSSWNGVKMHANQDLVTGYLKDTLKFKGFVISDWEGIDRITTPAGSDY
SYSVKASILAGLDMIMVPNKYQQFISILTGHVNGGVIPMSRIDDAVTRIL
RVKFTMGLFENPYADPAMAEQLGKQEHRDLAREAARKSLVLLKNGKTSTD
APLLPLPKKAPKILVAGSHADNLGYQCGGWTIEWQGDTGRTTVGTTILEA
VKAAVDPSTVVVFAENPDAEFVKSGGFSYAIVAVGEHPYTETKGDNLNLT
IPEPGLSTVQAVCGGVRCATVLISGRPVVVQPLLAASDALVAAWLPGSEG
QGVTDALFGDFGFTGRLPRTWFKSVDQLPMNVGDAHYDPLFRLGYGLTTN
AT

Ligand information

• Ligand ID: IDD
• InChI: InChI=1S/C14H16N2O4/c17-7-10-11(18)12(19)13(20)14-15-9(6-16(10)14)8-4-2-1-3-5-8/h1-6,10-13,17-20H,7H2/t10-,11-,12+,13-/m1/s1
• InChIKey: DLVNFMROYKHANV-FVCCEPFGSA-N
• SMILES:
  CACTVS 3.341: OC[CH]1[CH](O)[CH](O)[CH](O)c2nc(cn12)c3ccccc3
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)c2cn3c(n2)C(C(C(C3CO)O)O)O
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)c2cn3c(n2)[C@@H]([C@H]([C@@H]([C@H]3CO)O)O)O
  CACTVS 3.341: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)c2nc(cn12)c3ccccc3
  ACDLabs 10.04: OC2c1nc(cn1C(C(O)C2O)CO)c3ccccc3
• Formula: C14 H16 N2 O4
• Name: (5R,6R,7S,8S)-5-(HYDROXYMETHYL)-2-PHENYL-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL;
  GLUCO-PHENYLIMIDAZOLE
• DrugBank: DB02862
• ZINC: ZINC000033821368
• PDB chain: 1x38 Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1x38 Structural rationale for low-nanomolar binding of transition state mimics to a family GH3 beta-D-glucan glucohydrolase from barley.
• Resolution: 1.698 Å
• Binding residue (original residue number in PDB): D95 R158 K206 H207 M250 Y253 D285 W286 W434 E491
• Binding residue (residue number reindexed from 1): D95 R158 K206 H207 M250 Y253 D285 W286 W434 E491
• Annotation score: 1
• Binding affinity: MOAD: Ki=1.7nM
  PDBbind-CN: -logKd/Ki=8.77,Ki=1.7nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D285 E491
• Catalytic site (residue number reindexed from 1): D285 E491
• Enzyme Commision number: 3.2.1.21: beta-glucosidase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0016798 hydrolase activity, acting on glycosyl bonds

Biological Process

• GO:0005975 carbohydrate metabolic process

Cellular Component

• GO:0005576 extracellular region

External links

• PDB: RCSB:1x38, PDBe:1x38, PDBj:1x38
• PDBsum: 1x38
• PubMed: 16342944
• UniProt: Q9XEI3