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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3aiv

2.500 Å

X-ray

2010-05-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic
ID:HGGL_SECCE
AC:Q9FYS3
Organism:Secale cereale
Reign:Eukaryota
TaxID:4550
EC Number:3.2.1.182


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:17.437
Number of residues:26
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 0
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.837799.875

% Hydrophobic% Polar
48.9551.05
According to VolSite

Ligand :
3aiv_1 Structure
HET Code: HBO
Formula: C9H9NO5
Molecular weight: 211.171 g/mol
DrugBank ID: DB02185
Buried Surface Area:54.41 %
Polar Surface area: 79.23 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-55.0327-1.64953-2.51747


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
OHBOE2GLU- 1913.14120.36H-Bond
(Ligand Donor)
C5BCG2THR- 1944.50Hydrophobic
OHBOG1THR- 1943.43122.54H-Bond
(Protein Donor)
C9BCZPHE- 1983.610Hydrophobic
C7BCE2PHE- 1983.440Hydrophobic
C2BCZ2TRP- 3794.390Hydrophobic
C9BCD2TRP- 3793.870Hydrophobic
DuArDuArTRP- 3793.740Aromatic Face/Face
O3BOHOH- 5402.77179.98H-Bond
(Protein Donor)