scPDB - 2viy entry

Protein Data Bank Entry:

PDB ID : 2viy

Resolution :1.820 Å

Experimental Method : X-ray

Deposition Date : 2007-12-06

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:	18.688
Number of residues:	49
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.701	712.125

% Hydrophobic	% Polar
28.91	71.09
According to VolSite

Ligand :

HET Code:	VG3
Formula:	C31H46N3O5S
Molecular weight:	572.779 g/mol
DrugBank ID:	-
Buried Surface Area:	60.3 %
Polar Surface area:	137.55 Å2

Number of
H-Bond Acceptors:	5
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
30.6635	2.25105	34.5237

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
C15	CD1	LEU- 91	3.75	0	Hydrophobic	false
O19	OD2	ASP- 93	2.65	172.12	H-Bond (Ligand Donor)	false
N22	O	GLY- 95	3.09	135.29	H-Bond (Ligand Donor)	false
N39	O	GLY- 95	3.04	146.61	H-Bond (Ligand Donor)	false
C47	CB	SER- 96	3.52	0	Hydrophobic	false
C46	CG1	VAL- 130	3.61	0	Hydrophobic	false
C4	CD1	TYR- 132	3.97	0	Hydrophobic	false
C5	CD1	TYR- 132	3.91	0	Hydrophobic	false
C18	CB	TYR- 132	4.1	0	Hydrophobic	false
C46	CE1	TYR- 132	4.26	0	Hydrophobic	false
C47	CD1	TYR- 132	3.89	0	Hydrophobic	false
C12	CB	THR- 133	4.44	0	Hydrophobic	false
O41	N	THR- 133	3.37	142.54	H-Bond (Protein Donor)	false
O41	OG1	THR- 133	3.4	161.46	H-Bond (Protein Donor)	false
O6	N	GLN- 134	2.88	155.92	H-Bond (Protein Donor)	false
C7	CB	GLN- 134	3.65	0	Hydrophobic	false
C5	CD1	ILE- 179	3.71	0	Hydrophobic	false
C45	CG	ARG- 189	4.17	0	Hydrophobic	false
C43	CZ	TYR- 259	4.18	0	Hydrophobic	false
C24	CD1	ILE- 287	4	0	Hydrophobic	false
N22	OD1	ASP- 289	3.87	0	Ionic (Ligand Cationic)	false
N22	OD2	ASP- 289	2.66	0	Ionic (Ligand Cationic)	false
N22	OD2	ASP- 289	2.66	164.68	H-Bond (Ligand Donor)	false
N2	O	GLY- 291	2.86	166.11	H-Bond (Ligand Donor)	false
C12	CG2	THR- 292	4.03	0	Hydrophobic	false
C10	CB	THR- 293	3.8	0	Hydrophobic	false
O76	N	ASN- 294	3.08	153.14	H-Bond (Protein Donor)	false
C67	CB	SER- 386	4.15	0	Hydrophobic	false