scPDB - 3mpe entry

Protein Data Bank Entry:

PDB ID : 3mpe

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2010-04-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cathepsin S
ID:	CATS_HUMAN
AC:	P25774
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.22.27

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	23.044
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.538	303.750

% Hydrophobic	% Polar
52.22	47.78
According to VolSite

Ligand :

HET Code:	N2A
Formula:	C34H34Cl2FN6O3
Molecular weight:	664.577 g/mol
DrugBank ID:	-
Buried Surface Area:	42.04 %
Polar Surface area:	89.76 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	6
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-10.252	3.77307	-82.44

Binding mode :

What is Poseview ?

2D View
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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
F96	CG	LYS- 64	3.32	0	Hydrophobic	false
N77	O	GLY- 69	3.28	162.99	H-Bond (Ligand Donor)	false
C30	CD1	PHE- 70	3.45	0	Hydrophobic	false
C63	CE	MET- 71	3.79	0	Hydrophobic	false
CL73	SD	MET- 71	4.12	0	Hydrophobic	false
C22	CG2	THR- 73	4.48	0	Hydrophobic	false
C30	CG2	THR- 73	3.74	0	Hydrophobic	false
C60	CG2	VAL- 162	3.68	0	Hydrophobic	false
C41	CD1	PHE- 211	3.45	0	Hydrophobic	false
C62	CB	PHE- 211	4.41	0	Hydrophobic	false