scPDB - 3skg entry

Protein Data Bank Entry:

PDB ID : 3skg

Resolution :2.880 Å

Experimental Method : X-ray

Deposition Date : 2011-06-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-secretase 1
ID:	BACE1_HUMAN
AC:	P56817
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.23.46

Chains:

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

Ligand binding site composition:

B-Factor:	14.552
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.693	847.125

% Hydrophobic	% Polar
31.87	68.13
According to VolSite

Ligand :

HET Code:	PB8
Formula:	C38H47F2N4O4
Molecular weight:	661.801 g/mol
DrugBank ID:	-
Buried Surface Area:	55.09 %
Polar Surface area:	115.35 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
35.715	63.766	30.0595

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
C10	CD2	LEU- 30	4.23	0	Hydrophobic	false
C29	CD1	LEU- 30	4.03	0	Hydrophobic	false
F47	CD2	LEU- 30	4.43	0	Hydrophobic	false
O46	OD1	ASP- 32	3.36	136	H-Bond (Ligand Donor)	false
C6	CB	TYR- 71	4.37	0	Hydrophobic	false
C22	CD1	TYR- 71	3.73	0	Hydrophobic	false
C36	CD1	TYR- 71	4.4	0	Hydrophobic	false
F48	CD2	TYR- 71	3.69	0	Hydrophobic	false
C11	CB	TYR- 71	3.65	0	Hydrophobic	false
C6	CB	THR- 72	4.25	0	Hydrophobic	false
C34	CB	THR- 72	3.88	0	Hydrophobic	false
C4	CG2	THR- 72	3.78	0	Hydrophobic	false
C9	CB	GLN- 73	3.83	0	Hydrophobic	false
F48	CD1	PHE- 108	3.68	0	Hydrophobic	false
F47	CD1	ILE- 110	3.72	0	Hydrophobic	false
C37	CD1	ILE- 110	4.29	0	Hydrophobic	false
F47	CH2	TRP- 115	3.27	0	Hydrophobic	false
N39	OD2	ASP- 228	2.78	123.75	H-Bond (Ligand Donor)	false
N39	OD2	ASP- 228	2.78	0	Ionic (Ligand Cationic)	false
N42	O	GLY- 230	2.66	152.71	H-Bond (Ligand Donor)	false
N41	OG1	THR- 232	2.97	164.66	H-Bond (Ligand Donor)	false
O43	N	THR- 232	2.82	163.17	H-Bond (Protein Donor)	false
C8	CD	ARG- 235	4.23	0	Hydrophobic	false