scPDB - 2vie entry

Protein Data Bank Entry:

PDB ID : 2vie

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-11-30

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
A	100 %

Ligand binding site composition:

B-Factor:	18.813
Number of residues:	50
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.288	391.500

% Hydrophobic	% Polar
31.03	68.97
According to VolSite

Ligand :

HET Code:	VG0
Formula:	C32H49N4O3
Molecular weight:	537.756 g/mol
DrugBank ID:	-
Buried Surface Area:	68.88 %
Polar Surface area:	98.28 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
29.7344	1.69985	34.5572

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
C18	CD1	LEU- 91	3.54	0	Hydrophobic	false
O21	OD1	ASP- 93	3.39	150.11	H-Bond (Ligand Donor)	false
O21	OD2	ASP- 93	2.6	147.42	H-Bond (Ligand Donor)	false
N20	O	GLY- 95	3.44	145.82	H-Bond (Ligand Donor)	false
C83	CB	SER- 96	4.26	0	Hydrophobic	false
C79	CG1	VAL- 130	4.03	0	Hydrophobic	false
C4	CD1	TYR- 132	4.04	0	Hydrophobic	false
C5	CD1	TYR- 132	3.82	0	Hydrophobic	false
C15	CB	TYR- 132	4.04	0	Hydrophobic	false
C73	CD1	TYR- 132	4.27	0	Hydrophobic	false
O7	N	THR- 133	3.16	120.93	H-Bond (Protein Donor)	false
C9	CB	THR- 133	4.07	0	Hydrophobic	false
O7	N	GLN- 134	3	158.67	H-Bond (Protein Donor)	false
C8	CB	GLN- 134	3.78	0	Hydrophobic	false
C17	CD1	ILE- 171	4.36	0	Hydrophobic	false
C39	CD1	ILE- 171	4.1	0	Hydrophobic	false
C5	CD1	ILE- 179	3.66	0	Hydrophobic	false
C83	CD1	ILE- 187	4.18	0	Hydrophobic	false
C65	CE1	TYR- 259	3.58	0	Hydrophobic	false
C70	CE1	TYR- 259	4.31	0	Hydrophobic	false
C83	CE1	TYR- 259	4.26	0	Hydrophobic	false
C65	CD1	ILE- 287	3.47	0	Hydrophobic	false
N20	OD2	ASP- 289	2.66	173.55	H-Bond (Ligand Donor)	false
N20	OD2	ASP- 289	2.66	0	Ionic (Ligand Cationic)	false
N2	O	GLY- 291	2.92	164.16	H-Bond (Ligand Donor)	false
C9	CG2	THR- 292	4.21	0	Hydrophobic	false
C11	CB	THR- 293	4.03	0	Hydrophobic	false
C49	CB	ASN- 294	3.87	0	Hydrophobic	false
O57	N	ASN- 294	2.84	168.43	H-Bond (Protein Donor)	false
C49	CD	ARG- 296	3.83	0	Hydrophobic	false