scPDB - 3h8b entry

Protein Data Bank Entry:

PDB ID : 3h8b

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2009-04-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cathepsin L1
ID:	CATL1_HUMAN
AC:	P07711
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.22.15

Chains:

Chain Name:	Percentage of Residues within binding site
B	19 %
C	15 %
F	66 %

Ligand binding site composition:

B-Factor:	21.184
Number of residues:	61
Including
Standard Amino Acids:	59
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.440	1248.750

% Hydrophobic	% Polar
42.16	57.84
According to VolSite

Ligand :

HET Code:	NSY
Formula:	C57H65N8O5
Molecular weight:	942.177 g/mol
DrugBank ID:	-
Buried Surface Area:	53.4 %
Polar Surface area:	209.14 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	8
Rings:	6
Aromatic rings:	6
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	4
Rotatable Bonds:	27

Mass center Coordinates

X	Y	Z
10.2524	-14.2062	75.8287

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
C53	CD	ARG- 8	4.1	0	Hydrophobic	false
C52	CB	ARG- 8	3.76	0	Hydrophobic	false
C56	CG	GLU- 9	3.9	0	Hydrophobic	false
C14	CB	GLN- 21	4.22	0	Hydrophobic	false
C64	CG	GLN- 21	4.17	0	Hydrophobic	false
C5	CB	GLN- 21	3.61	0	Hydrophobic	false
C27	CG	GLN- 21	3.48	0	Hydrophobic	false
C55	CG	GLU- 63	3.33	0	Hydrophobic	false
O39	N	GLY- 68	2.74	143.68	H-Bond (Protein Donor)	false
N60	O	GLY- 68	3.11	166.99	H-Bond (Ligand Donor)	false
C48	CD2	LEU- 69	3.48	0	Hydrophobic	false
C50	CD2	LEU- 69	3.51	0	Hydrophobic	false
C53	CG	LEU- 69	4.01	0	Hydrophobic	false
C46	SD	MET- 70	3.52	0	Hydrophobic	false
C48	CE	MET- 70	3.39	0	Hydrophobic	false
C49	CB	ALA- 135	3.35	0	Hydrophobic	false
C50	CB	ALA- 135	3.72	0	Hydrophobic	false
C47	CB	ALA- 135	3.44	0	Hydrophobic	false
C62	CG	GLU- 141	3.58	0	Hydrophobic	false
C64	CG	GLU- 141	3.52	0	Hydrophobic	false
C24	CD2	LEU- 144	3.78	0	Hydrophobic	false
C26	CB	LEU- 144	3.96	0	Hydrophobic	false
C63	CD2	LEU- 144	3.34	0	Hydrophobic	false
C63	CD1	LEU- 144	4.36	0	Hydrophobic	false
C47	CB	MET- 161	4.48	0	Hydrophobic	false
N40	O	ASP- 162	3.1	155.32	H-Bond (Ligand Donor)	false
C50	CB	ALA- 214	3.87	0	Hydrophobic	false