scPDB - 2va6 entry

Protein Data Bank Entry:

PDB ID : 2va6

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-08-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.570	6.570	6.570	0.000	6.570	1

List of CHEMBLId :

CHEMBL1233206

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:	35.666
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.509	560.250

% Hydrophobic	% Polar
34.34	65.66
According to VolSite

Ligand :

HET Code:	H24
Formula:	C19H22N3O2
Molecular weight:	324.397 g/mol
DrugBank ID:	DB07874
Buried Surface Area:	58.59 %
Polar Surface area:	69.53 Å2

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

Mass center Coordinates

X	Y	Z
70.0247	48.2082	6.64779

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
C3	CD1	LEU- 30	4.22	0	Hydrophobic	false
C8	CD2	LEU- 30	3.83	0	Hydrophobic	false
N24	OD1	ASP- 32	2.83	166.69	H-Bond (Ligand Donor)	false
C15	CB	SER- 35	4.29	0	Hydrophobic	false
C15	CZ	TYR- 71	4.13	0	Hydrophobic	false
C18	CE2	TYR- 71	3.5	0	Hydrophobic	false
C5	CD1	ILE- 110	4.15	0	Hydrophobic	false
C15	CD1	ILE- 118	3.38	0	Hydrophobic	false
N24	OD2	ASP- 228	2.64	145.61	H-Bond (Ligand Donor)	false
C1	CB	ALA- 335	4.49	0	Hydrophobic	false