scPDB - 4pry entry

Protein Data Bank Entry:

PDB ID : 4pry

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2014-03-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
A	100 %

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

Ligandability	Volume (Å3)
0.058	381.375

% Hydrophobic	% Polar
35.40	64.60
According to VolSite

Ligand :

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

X	Y	Z
38.6748	10.9707	70.1842

Binding mode :

What is Poseview ?

2D View
3D View

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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
CB	SG	CYS- 163	4.38	0	Hydrophobic	false
CB	CD1	TYR- 204	3.6	0	Hydrophobic	false
CG2	CZ3	TRP- 206	3.85	0	Hydrophobic	false
CG	CE3	TRP- 206	3.64	0	Hydrophobic	false
N	O	ARG- 207	2.86	172.42	H-Bond (Ligand Donor)	false
O	N	ARG- 207	2.87	152	H-Bond (Protein Donor)	false
OE1	NH1	ARG- 207	2.76	169.86	H-Bond (Protein Donor)	false
OE1	CZ	ARG- 207	3.68	0	Ionic (Protein Cationic)	false
CD1	CB	ASN- 208	4.29	0	Hydrophobic	false
CD1	CZ2	TRP- 214	4.09	0	Hydrophobic	false
CD2	CZ2	TRP- 214	4.25	0	Hydrophobic	false
CD2	CB	SER- 249	3.73	0	Hydrophobic	false