scPDB - 2vj7 entry

Protein Data Bank Entry:

PDB ID : 2vj7

Resolution :1.600 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:	14.980
Number of residues:	48
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.885	769.500

% Hydrophobic	% Polar
39.47	60.53
According to VolSite

Ligand :

HET Code:	VG6
Formula:	C31H36F3N4O3
Molecular weight:	569.638 g/mol
DrugBank ID:	-
Buried Surface Area:	69.5 %
Polar Surface area:	98.28 Å2

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

Mass center Coordinates

X	Y	Z
29.9741	2.32159	34.0224

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
C18	CD1	LEU- 91	3.48	0	Hydrophobic	false
O13	OD1	ASP- 93	3.47	137.63	H-Bond (Ligand Donor)	false
O13	OD2	ASP- 93	2.59	162.57	H-Bond (Ligand Donor)	false
N16	O	GLY- 95	3.04	147.53	H-Bond (Ligand Donor)	false
F75	CB	SER- 96	3.42	0	Hydrophobic	false
F75	CG1	VAL- 130	3.69	0	Hydrophobic	false
F76	CG1	VAL- 130	4.2	0	Hydrophobic	false
C11	CD1	TYR- 132	3.29	0	Hydrophobic	false
C12	CD1	TYR- 132	4.03	0	Hydrophobic	false
C21	CB	TYR- 132	4.25	0	Hydrophobic	false
C73	CD1	TYR- 132	4.45	0	Hydrophobic	false
F75	CE1	TYR- 132	3.43	0	Hydrophobic	false
C4	CB	THR- 133	4.29	0	Hydrophobic	false
O9	N	GLN- 134	2.94	159.94	H-Bond (Protein Donor)	false
C3	CB	GLN- 134	3.69	0	Hydrophobic	false
C19	CD1	ILE- 171	4.49	0	Hydrophobic	false
C39	CD1	ILE- 171	4.22	0	Hydrophobic	false
C17	CD1	ILE- 179	3.74	0	Hydrophobic	false
F74	CD1	ILE- 187	3.84	0	Hydrophobic	false
F74	CE1	TYR- 259	4.22	0	Hydrophobic	false
N16	OD1	ASP- 289	3.75	0	Ionic (Ligand Cationic)	false
N16	OD2	ASP- 289	2.58	0	Ionic (Ligand Cationic)	false
N16	OD2	ASP- 289	2.58	177.27	H-Bond (Ligand Donor)	false
N8	O	GLY- 291	3	160.38	H-Bond (Ligand Donor)	false
C3	CB	THR- 292	4.45	0	Hydrophobic	false
C4	CG2	THR- 292	4.02	0	Hydrophobic	false
N38	OG1	THR- 293	3.11	125.09	H-Bond (Ligand Donor)	false
O58	N	THR- 293	3.35	120.52	H-Bond (Protein Donor)	false
C6	CB	THR- 293	4.08	0	Hydrophobic	false
C49	CB	ASN- 294	3.95	0	Hydrophobic	false
O58	N	ASN- 294	2.85	157.16	H-Bond (Protein Donor)	false
C49	CD	ARG- 296	3.75	0	Hydrophobic	false