scPDB - 3dv5 entry

Protein Data Bank Entry:

PDB ID : 3dv5

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:	39.683
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.270	1306.125

% Hydrophobic	% Polar
36.18	63.82
According to VolSite

Ligand :

HET Code:	BAV
Formula:	C29H50N3O3
Molecular weight:	488.726 g/mol
DrugBank ID:	-
Buried Surface Area:	66.79 %
Polar Surface area:	86.25 Å2

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

Mass center Coordinates

X	Y	Z
30.1696	5.77157	14.444

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
C23	CD2	LEU- 30	3.78	0	Hydrophobic	false
C26	CD1	LEU- 30	4.27	0	Hydrophobic	false
C14	CD2	LEU- 30	3.8	0	Hydrophobic	false
O46	OD2	ASP- 32	2.63	154.12	H-Bond (Ligand Donor)	false
N51	O	GLY- 34	3.19	149.83	H-Bond (Ligand Donor)	false
C72	CB	SER- 35	3.6	0	Hydrophobic	false
C72	CG1	VAL- 69	3.52	0	Hydrophobic	false
C9	CD1	TYR- 71	3.96	0	Hydrophobic	false
C40	CG	TYR- 71	3.55	0	Hydrophobic	false
C44	CD1	TYR- 71	3.96	0	Hydrophobic	false
C72	CD1	TYR- 71	3.36	0	Hydrophobic	false
C64	CB	THR- 72	4.22	0	Hydrophobic	false
C77	CB	THR- 72	3.67	0	Hydrophobic	false
O76	N	GLN- 73	3.36	151.02	H-Bond (Protein Donor)	false
C77	CB	GLN- 73	3.84	0	Hydrophobic	false
C40	CE1	PHE- 108	4.14	0	Hydrophobic	false
C17	CE1	PHE- 108	3.85	0	Hydrophobic	false
C20	CD1	ILE- 110	4.48	0	Hydrophobic	false
C29	CD1	ILE- 110	3.98	0	Hydrophobic	false
C17	CH2	TRP- 115	3.66	0	Hydrophobic	false
C20	CZ2	TRP- 115	3.86	0	Hydrophobic	false
C9	CD1	ILE- 118	4.4	0	Hydrophobic	false
C14	CD1	ILE- 118	3.89	0	Hydrophobic	false
C68	CB	ILE- 126	3.98	0	Hydrophobic	false
C68	CE1	TYR- 198	4.09	0	Hydrophobic	false
N51	OD2	ASP- 228	2.65	169.96	H-Bond (Ligand Donor)	false
N51	OD2	ASP- 228	2.65	0	Ionic (Ligand Cationic)	false
N51	OD1	ASP- 228	3.98	0	Ionic (Ligand Cationic)	false
N5	O	GLY- 230	3.03	158.79	H-Bond (Ligand Donor)	false
C35	CB	THR- 232	4.36	0	Hydrophobic	false
O39	N	THR- 232	2.85	164.77	H-Bond (Protein Donor)	false