Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1vrq

2.200 Å

X-ray

2005-04-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Subunit alpha of sarocosine oxidase
ID:Q50LF0_9CORY
AC:Q50LF0
Organism:Corynebacterium sp. U-96
Reign:Bacteria
TaxID:31944
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:33.823
Number of residues:39
Including
Standard Amino Acids: 38
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.7741738.125

% Hydrophobic% Polar
56.3143.69
According to VolSite

Ligand :
1vrq_1 Structure
HET Code: FON
Formula: C20H21N7O7
Molecular weight: 471.423 g/mol
DrugBank ID: DB03256
Buried Surface Area:55.64 %
Polar Surface area: 221.2 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 5
Rings: 3
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 9

Mass center Coordinates

XYZ
-26.763950.1544-0.106941


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
C9CE1TYR- 6634.070Hydrophobic
C15CD1TYR- 6632.920Hydrophobic
C11CBTYR- 6634.210Hydrophobic
C13CG2VAL- 6783.910Hydrophobic
N8OTHR- 6913.23163.9H-Bond
(Ligand Donor)
C13CG2ILE- 7744.430Hydrophobic
C9CE1PHE- 7764.260Hydrophobic
NA2OE1GLU- 7832.72141.24H-Bond
(Ligand Donor)
N3OE1GLU- 7833.36124.36H-Bond
(Ligand Donor)
N3OE2GLU- 7832.7139.93H-Bond
(Ligand Donor)
OE2NZLYS- 8223.840Ionic
(Protein Cationic)
CBCE1PHE- 8244.220Hydrophobic
CGCZPHE- 8243.930Hydrophobic