Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3lit

2.190 Å

X-ray

2010-01-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Protease
ID:Q82134_9DELA
AC:Q82134
Organism:Human T-lymphotropic virus 1
Reign:Viruses
TaxID:11908
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A50 %
B50 %


Ligand binding site composition:

B-Factor:35.988
Number of residues:42
Including
Standard Amino Acids: 40
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.052938.250

% Hydrophobic% Polar
46.4053.60
According to VolSite

Ligand :
3lit_1 Structure
HET Code: E15
Formula: C35H52N5O5S
Molecular weight: 654.883 g/mol
DrugBank ID: -
Buried Surface Area:62.77 %
Polar Surface area: 180.77 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 13

Mass center Coordinates

XYZ
20.424733.627725.8218


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
CAUCDARG- 103.760Hydrophobic
DuArCZARG- 103.9106.41Pi/Cation
CBACD2LEU- 304.430Hydrophobic
CAICD2LEU- 303.530Hydrophobic
OANOD2ASP- 322.84146.12H-Bond
(Protein Donor)
OAOOD2ASP- 322.94121.92H-Bond
(Protein Donor)
OAOOD1ASP- 322.75162.96H-Bond
(Ligand Donor)
OAOOD2ASP- 323.19133.15H-Bond
(Ligand Donor)
NBCOGLY- 343.18161.89H-Bond
(Ligand Donor)
CABCBALA- 354.230Hydrophobic
CACCBALA- 354.040Hydrophobic
CG2CBALA- 353.840Hydrophobic
NAJOD2ASP- 362.68161.43H-Bond
(Ligand Donor)
NAJOD2ASP- 362.680Ionic
(Ligand Cationic)
OAKNASP- 363.04168.91H-Bond
(Protein Donor)
CG2CG2VAL- 394.170Hydrophobic
CBSCG2VAL- 394.250Hydrophobic
CG1CG1VAL- 563.520Hydrophobic
CAACG1VAL- 563.20Hydrophobic
NOLEU- 573.12154.57H-Bond
(Ligand Donor)
CATCD2LEU- 573.710Hydrophobic
CG1CBALA- 593.50Hydrophobic
CABCBALA- 594.430Hydrophobic
CARCBALA- 593.70Hydrophobic
CAGCD1LEU- 913.910Hydrophobic
CAACD1LEU- 914.470Hydrophobic
CACCD1LEU- 913.710Hydrophobic
SBECZ3TRP- 983.920Hydrophobic
CAPCZ2TRP- 983.350Hydrophobic
CG2CD1ILE- 1004.310Hydrophobic
CARCD1ILE- 1004.30Hydrophobic
SBECD1ILE- 1004.340Hydrophobic
CABCD1ILE- 1004.240Hydrophobic
CAVCD1ILE- 1003.780Hydrophobic
NBBOHOH- 1392.79166.59H-Bond
(Ligand Donor)