scPDB - 3vg1 entry

Protein Data Bank Entry:

PDB ID : 3vg1

Resolution :1.770 Å

Experimental Method : X-ray

Deposition Date : 2012-01-10

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:	19.099
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.759	992.250

% Hydrophobic	% Polar
28.91	71.09
According to VolSite

Ligand :

HET Code:	0GT
Formula:	C27H34F2N2O3S
Molecular weight:	504.632 g/mol
DrugBank ID:	-
Buried Surface Area:	65.73 %
Polar Surface area:	90.57 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
30.3075	71.6019	18.7054

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	CD2	LEU- 30	3.59	0	Hydrophobic	false
O68	OD2	ASP- 32	2.52	160.99	H-Bond (Ligand Donor)	false
N40	O	GLY- 34	2.97	141.37	H-Bond (Ligand Donor)	false
C60	CB	SER- 35	3.78	0	Hydrophobic	false
C56	CG1	VAL- 69	4.29	0	Hydrophobic	false
C60	CG1	VAL- 69	3.57	0	Hydrophobic	false
C18	CB	TYR- 71	4.29	0	Hydrophobic	false
C60	CE1	TYR- 71	3.62	0	Hydrophobic	false
C25	CD1	TYR- 71	3.75	0	Hydrophobic	false
O38	N	THR- 72	2.93	133.49	H-Bond (Protein Donor)	false
C53	CB	THR- 72	4.45	0	Hydrophobic	false
N11	O	PHE- 108	2.88	135.61	H-Bond (Ligand Donor)	false
C5	CD1	ILE- 110	3.73	0	Hydrophobic	false
C5	CZ2	TRP- 115	4.03	0	Hydrophobic	false
C22	CD1	ILE- 118	4.02	0	Hydrophobic	false
C64	CD1	ILE- 126	3.89	0	Hydrophobic	false
C64	CE1	TYR- 186	4.32	0	Hydrophobic	false
N40	OD2	ASP- 216	2.76	163.27	H-Bond (Ligand Donor)	false
N40	OD2	ASP- 216	2.76	0	Ionic (Ligand Cationic)	false
C31	CB	THR- 219	4.43	0	Hydrophobic	false
F1	CB	THR- 220	4.37	0	Hydrophobic	false
O39	NH2	ARG- 223	2.76	133.75	H-Bond (Protein Donor)	false