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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:

4pry

1.700 Å

X-ray

2014-03-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Caspase-3
ID:CASP3_HUMAN
AC:P42574
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.4.22.56


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.404
Number of residues:37
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.058381.375

% Hydrophobic% Polar
35.4064.60
According to VolSite

Ligand :
4pry_1 Structure
HET Code: LEU_GLU_THR_ACE_ASA
Formula: C15H27N3O6
Molecular weight: 345.391 g/mol
DrugBank ID: -
Buried Surface Area:56.35 %
Polar Surface area: 163.26 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 4
Rings: 0
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 11

Mass center Coordinates

XYZ
38.674810.970770.1842


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
CBSGCYS- 1634.380Hydrophobic
CBCD1TYR- 2043.60Hydrophobic
CG2CZ3TRP- 2063.850Hydrophobic
CGCE3TRP- 2063.640Hydrophobic
NOARG- 2072.86172.42H-Bond
(Ligand Donor)
ONARG- 2072.87152H-Bond
(Protein Donor)
OE1NH1ARG- 2072.76169.86H-Bond
(Protein Donor)
OE1CZARG- 2073.680Ionic
(Protein Cationic)
CD1CBASN- 2084.290Hydrophobic
CD1CZ2TRP- 2144.090Hydrophobic
CD2CZ2TRP- 2144.250Hydrophobic
CD2CBSER- 2493.730Hydrophobic