scPDB - 3dv1 entry

Protein Data Bank Entry:

PDB ID : 3dv1

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2008-07-18

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:	38.412
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.924	934.875

% Hydrophobic	% Polar
32.49	67.51
According to VolSite

Ligand :

HET Code:	AR9
Formula:	C24H45N3O4
Molecular weight:	439.632 g/mol
DrugBank ID:	-
Buried Surface Area:	66.09 %
Polar Surface area:	107.52 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
30.7835	6.20013	15.2629

Binding mode :

What is Poseview ?

2D View
3D View

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
C10	CD2	LEU- 30	4.22	0	Hydrophobic	false
C13	CD1	LEU- 30	3.45	0	Hydrophobic	false
O49	OD1	ASP- 32	2.5	174.45	H-Bond (Protein Donor)	false
N62	O	GLY- 34	2.87	175.34	H-Bond (Ligand Donor)	false
C67	CB	SER- 35	4.1	0	Hydrophobic	false
C73	CG1	VAL- 69	3.86	0	Hydrophobic	false
C5	CD1	TYR- 71	4.34	0	Hydrophobic	false
C43	CD2	TYR- 71	3.48	0	Hydrophobic	false
C47	CD1	TYR- 71	3.93	0	Hydrophobic	false
C51	CB	TYR- 71	4.49	0	Hydrophobic	false
C38	CB	THR- 72	3.81	0	Hydrophobic	false
C51	CB	THR- 72	4.42	0	Hydrophobic	false
O61	N	THR- 72	2.98	139.47	H-Bond (Protein Donor)	false
O37	N	GLN- 73	3.04	142.58	H-Bond (Protein Donor)	false
C38	CB	GLN- 73	3.91	0	Hydrophobic	false
C10	CE1	PHE- 108	4.33	0	Hydrophobic	false
C43	CD1	PHE- 108	3.77	0	Hydrophobic	false
C25	CD1	ILE- 110	4.11	0	Hydrophobic	false
C19	CD1	ILE- 110	3.77	0	Hydrophobic	false
C10	CH2	TRP- 115	4.32	0	Hydrophobic	false
C16	CZ2	TRP- 115	3.97	0	Hydrophobic	false
C5	CD1	ILE- 118	4.38	0	Hydrophobic	false
C10	CD1	ILE- 118	4.35	0	Hydrophobic	false
C67	CD1	ILE- 126	4.23	0	Hydrophobic	false
C70	CB	ILE- 126	4.19	0	Hydrophobic	false
C73	CG	ARG- 128	4.35	0	Hydrophobic	false
C56	CE1	TYR- 198	4.43	0	Hydrophobic	false
C67	CE1	TYR- 198	3.92	0	Hydrophobic	false
C56	CD1	ILE- 226	4.01	0	Hydrophobic	false
O49	OD2	ASP- 228	2.6	160.65	H-Bond (Ligand Donor)	false
N1	O	GLY- 230	3.02	167.6	H-Bond (Ligand Donor)	false
C28	CB	THR- 232	4.44	0	Hydrophobic	false
O42	N	THR- 232	2.93	170.92	H-Bond (Protein Donor)	false