scPDB - 2vj6 entry

Protein Data Bank Entry:

PDB ID : 2vj6

Resolution :1.800 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:	17.733
Number of residues:	48
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.893	894.375

% Hydrophobic	% Polar
32.83	67.17
According to VolSite

Ligand :

HET Code:	VG5
Formula:	C32H46N5O4
Molecular weight:	564.739 g/mol
DrugBank ID:	-
Buried Surface Area:	68.41 %
Polar Surface area:	127.37 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
30.038	2.24078	34.1567

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
C57	CD1	LEU- 91	3.65	0	Hydrophobic	false
O13	OD1	ASP- 93	3.46	132.56	H-Bond (Ligand Donor)	false
O13	OD2	ASP- 93	2.6	172.99	H-Bond (Ligand Donor)	false
N16	O	GLY- 95	3.08	136.85	H-Bond (Ligand Donor)	false
N19	O	GLY- 95	2.97	159.06	H-Bond (Ligand Donor)	false
C27	CB	SER- 96	3.43	0	Hydrophobic	false
C26	CG1	VAL- 130	3.52	0	Hydrophobic	false
C11	CD1	TYR- 132	3.87	0	Hydrophobic	false
C12	CD1	TYR- 132	4.01	0	Hydrophobic	false
C26	CE1	TYR- 132	4.24	0	Hydrophobic	false
C27	CD1	TYR- 132	3.88	0	Hydrophobic	false
C60	CB	TYR- 132	4.11	0	Hydrophobic	false
C2	CB	THR- 133	4.01	0	Hydrophobic	false
C79	CG2	THR- 133	4.49	0	Hydrophobic	false
O9	N	GLN- 134	2.93	163.29	H-Bond (Protein Donor)	false
C3	CB	GLN- 134	3.63	0	Hydrophobic	false
C58	CD1	ILE- 171	4.37	0	Hydrophobic	false
C67	CD1	ILE- 171	4	0	Hydrophobic	false
C11	CD1	ILE- 179	3.62	0	Hydrophobic	false
C25	CG	ARG- 189	4.21	0	Hydrophobic	false
C23	CZ	TYR- 259	4.25	0	Hydrophobic	false
C22	CD1	ILE- 287	4.16	0	Hydrophobic	false
N16	OD1	ASP- 289	3.89	0	Ionic (Ligand Cationic)	false
N16	OD2	ASP- 289	2.71	0	Ionic (Ligand Cationic)	false
N16	OD2	ASP- 289	2.71	156.25	H-Bond (Ligand Donor)	false
N8	O	GLY- 291	2.83	167.24	H-Bond (Ligand Donor)	false
C2	CG2	THR- 292	4.07	0	Hydrophobic	false
C3	CB	THR- 292	4.46	0	Hydrophobic	false
N1	OG1	THR- 293	3.11	120.04	H-Bond (Ligand Donor)	false
C6	CB	THR- 293	3.98	0	Hydrophobic	false
C80	CB	ASN- 294	3.87	0	Hydrophobic	false
O88	N	ASN- 294	2.79	153.72	H-Bond (Protein Donor)	false
C80	CD	ARG- 296	3.83	0	Hydrophobic	false