Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3v1s

2.330 Å

X-ray

2011-12-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Strictosidine synthase
ID:STSY_RAUSE
AC:P68175
Organism:Rauvolfia serpentina
Reign:Eukaryota
TaxID:4060
EC Number:4.3.3.2


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:59.389
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.021621.000

% Hydrophobic% Polar
56.5243.48
According to VolSite

Ligand :
3v1s_2 Structure
HET Code: 0LH
Formula: C10H13N2
Molecular weight: 161.224 g/mol
DrugBank ID: -
Buried Surface Area:60.36 %
Polar Surface area: 32.57 Å2
Number of
H-Bond Acceptors: 0
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-27.297745.5988.19725


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
CADCG2VAL- 1764.350Hydrophobic
CABCG1VAL- 1763.860Hydrophobic
CADCD1ILE- 1793.890Hydrophobic
CABCG2ILE- 1793.920Hydrophobic
CACSDMET- 1803.930Hydrophobic
CAJCG1VAL- 2083.650Hydrophobic
CAICD1PHE- 2263.860Hydrophobic
NAAOE2GLU- 3093.16154.05H-Bond
(Ligand Donor)
NAAOE2GLU- 3093.160Ionic
(Ligand Cationic)
NAAOE1GLU- 3093.380Ionic
(Ligand Cationic)