scPDB - 3vf3 entry

Protein Data Bank Entry:

PDB ID : 3vf3

Resolution :1.480 Å

Experimental Method : X-ray

Deposition Date : 2012-01-09

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:	17.473
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.725	914.625

% Hydrophobic	% Polar
28.04	71.96
According to VolSite

Ligand :

HET Code:	0GS
Formula:	C21H24BrF3N2O3S
Molecular weight:	521.391 g/mol
DrugBank ID:	-
Buried Surface Area:	65.7 %
Polar Surface area:	100.8 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
30.5844	71.425	19.506

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
C2	CD2	LEU- 30	3.94	0	Hydrophobic	false
C8	CD2	LEU- 30	3.48	0	Hydrophobic	false
O50	OD2	ASP- 32	2.63	165.58	H-Bond (Ligand Donor)	false
N28	O	GLY- 34	2.99	142.13	H-Bond (Ligand Donor)	false
F44	CB	SER- 35	3.59	0	Hydrophobic	false
F45	CG1	VAL- 69	3.71	0	Hydrophobic	false
C5	CB	TYR- 71	4.34	0	Hydrophobic	false
C15	CD1	TYR- 71	4.06	0	Hydrophobic	false
F45	CD1	TYR- 71	3.9	0	Hydrophobic	false
F52	CD2	TYR- 71	4.17	0	Hydrophobic	false
C13	CD1	TYR- 71	3.76	0	Hydrophobic	false
O27	N	THR- 72	2.97	130.33	H-Bond (Protein Donor)	false
F52	CE1	PHE- 108	3.7	0	Hydrophobic	false
BR1	CZ2	TRP- 115	3.64	0	Hydrophobic	false
C10	CD1	ILE- 118	3.78	0	Hydrophobic	false
F44	CD1	ILE- 126	3.89	0	Hydrophobic	false
C46	CB	ILE- 126	4.5	0	Hydrophobic	false
N28	OD2	ASP- 215	2.81	169.02	H-Bond (Ligand Donor)	false
N28	OD2	ASP- 215	2.81	0	Ionic (Ligand Cationic)	false
C19	CB	THR- 218	4.48	0	Hydrophobic	false