scPDB - 3h89 entry

Protein Data Bank Entry:

PDB ID : 3h89

Resolution :2.500 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
D	100 %

Ligand binding site composition:

B-Factor:	19.955
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.708	344.250

% Hydrophobic	% Polar
50.98	49.02
According to VolSite

Ligand :

HET Code:	NSX
Formula:	C57H65N8O6
Molecular weight:	958.176 g/mol
DrugBank ID:	-
Buried Surface Area:	41.77 %
Polar Surface area:	229.36 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	9
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
72.7131	33.4273	92.926

Binding mode :

What is Poseview ?

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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
C56	CG	GLU- 63	3.72	0	Hydrophobic	false
O39	N	GLY- 68	2.66	156.77	H-Bond (Protein Donor)	false
N60	O	GLY- 68	3.12	146.44	H-Bond (Ligand Donor)	false
C48	CD2	LEU- 69	3.53	0	Hydrophobic	false
C50	CD2	LEU- 69	3.67	0	Hydrophobic	false
C53	CG	LEU- 69	3.78	0	Hydrophobic	false
C46	SD	MET- 70	3.49	0	Hydrophobic	false
C49	CB	ALA- 135	3.53	0	Hydrophobic	false
N72	O	ALA- 138	2.87	161.3	H-Bond (Ligand Donor)	false
C62	CG	GLU- 141	3.61	0	Hydrophobic	false
C63	CG	GLU- 141	3.23	0	Hydrophobic	false
C14	CD1	LEU- 144	3.28	0	Hydrophobic	false
C12	CD1	LEU- 144	3.68	0	Hydrophobic	false
C15	CD2	LEU- 144	3.29	0	Hydrophobic	false
C11	CD1	LEU- 144	4.18	0	Hydrophobic	false
C65	CZ	PHE- 145	3.16	0	Hydrophobic	false
C47	CB	MET- 161	4.42	0	Hydrophobic	false
N29	O	ASP- 162	3.33	123.39	H-Bond (Ligand Donor)	false
N40	O	ASP- 162	3.26	163.75	H-Bond (Ligand Donor)	false
O3	NE1	TRP- 189	3.09	157.57	H-Bond (Protein Donor)	false
C50	CB	ALA- 214	3.77	0	Hydrophobic	false