Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

5dsy

2.700 Å

X-ray

2015-09-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Poly [ADP-ribose] polymerase 2
ID:PARP2_HUMAN
AC:Q9UGN5
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.4.2.30


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:48.783
Number of residues:36
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.017850.500

% Hydrophobic% Polar
44.0555.95
According to VolSite

Ligand :
5dsy_3 Structure
HET Code: UHB
Formula: C24H28N9O6
Molecular weight: 538.536 g/mol
DrugBank ID: -
Buried Surface Area:60.84 %
Polar Surface area: 202.25 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 6
Rings: 6
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 5

Mass center Coordinates

XYZ
14.03119.4586710.4709


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
O29NE2HIS- 4152.53162.92H-Bond
(Protein Donor)
N09OGLY- 4162.9158.9H-Bond
(Ligand Donor)
O10NGLY- 4162.73170.69H-Bond
(Protein Donor)
O29OGSER- 4173.03170H-Bond
(Ligand Donor)
N39OGLY- 4293.09124.95H-Bond
(Ligand Donor)
N34NARG- 4312.99163.8H-Bond
(Protein Donor)
C03CBTYR- 4493.540Hydrophobic
C01CBALA- 4514.20Hydrophobic
O10OGSER- 4572.91167.04H-Bond
(Protein Donor)
C02CBGLU- 5453.880Hydrophobic