scPDB - 3r7n entry

Protein Data Bank Entry:

PDB ID : 3r7n

Resolution :2.330 Å

Experimental Method : X-ray

Deposition Date : 2011-03-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Caspase-2
ID:	CASP2_HUMAN
AC:	P42575
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.22.55

Chains:

Chain Name:	Percentage of Residues within binding site
C	44 %
D	56 %

Ligand binding site composition:

B-Factor:	19.544
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.434	573.750

% Hydrophobic	% Polar
41.18	58.82
According to VolSite

Ligand :

HET Code:	ASP_VAL_ALA_ACE_ASA
Formula:	C12H21N3O5
Molecular weight:	287.312 g/mol
DrugBank ID:	-
Buried Surface Area:	64.05 %
Polar Surface area:	143.04 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
1.04774	-24.6952	23.8222

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- 320	4.19	0	Hydrophobic	false
CB	CB	ALA- 375	4	0	Hydrophobic	false
CB	CE	MET- 377	3.99	0	Hydrophobic	false
N	O	ARG- 378	3	162.24	H-Bond (Ligand Donor)	false
O	N	ARG- 378	2.78	151	H-Bond (Protein Donor)	false
CG2	CB	ARG- 378	4.42	0	Hydrophobic	false
OD1	ND2	ASN- 379	3.07	153.42	H-Bond (Protein Donor)	false
CG1	CG2	THR- 380	4.17	0	Hydrophobic	false
CG2	CG2	THR- 380	4.3	0	Hydrophobic	false
CB	CZ2	TRP- 385	4.23	0	Hydrophobic	false
OD1	NE1	TRP- 385	3	177.85	H-Bond (Protein Donor)	false
N	O	TYR- 420	3.27	163.15	H-Bond (Ligand Donor)	false
OD2	N	TYR- 420	2.84	164.61	H-Bond (Protein Donor)	false
CB	CZ	PHE- 426	3.63	0	Hydrophobic	false
OD2	O	HOH- 517	2.94	180	H-Bond (Protein Donor)	false