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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:

1v08

1.900 Å

X-ray

2004-03-25

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 1, chloroplastic
ID:HGGL1_MAIZE
AC:P49235
Organism:Zea mays
Reign:Eukaryota
TaxID:4577
EC Number:3.2.1.182


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:19.848
Number of residues:24
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.882870.750

% Hydrophobic% Polar
58.9141.09
According to VolSite

Ligand :
1v08_2 Structure
HET Code: NTZ
Formula: C6H10N4O4
Molecular weight: 202.168 g/mol
DrugBank ID: DB02471
Buried Surface Area:56.14 %
Polar Surface area: 124.52 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 4
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
22.340454.6701-0.484214


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
O2OG1THR- 1942.95166.89H-Bond
(Ligand Donor)
C2CG2THR- 1943.540Hydrophobic
C6CE1PHE- 19840Hydrophobic
C4CZPHE- 2054.140Hydrophobic
C3CZ2TRP- 3784.20Hydrophobic
C5CE2TRP- 3783.740Hydrophobic
O4OE2GLU- 4643.3120.91H-Bond
(Ligand Donor)
C6CZPHE- 4663.630Hydrophobic