scPDB - 2vij entry

Protein Data Bank Entry:

PDB ID : 2vij

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2007-12-04

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:	18.796
Number of residues:	48
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.565	695.250

% Hydrophobic	% Polar
31.55	68.45
According to VolSite

Ligand :

HET Code:	C44
Formula:	C33H43N4O4S
Molecular weight:	591.784 g/mol
DrugBank ID:	-
Buried Surface Area:	65.61 %
Polar Surface area:	123.73 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
30.1479	1.80814	35.1061

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
C18	CD1	LEU- 91	3.68	0	Hydrophobic	false
O82	OD1	ASP- 93	3.49	142.86	H-Bond (Ligand Donor)	false
O82	OD2	ASP- 93	2.66	161.26	H-Bond (Ligand Donor)	false
N20	O	GLY- 95	3	146.75	H-Bond (Ligand Donor)	false
C4	CD1	TYR- 132	4.07	0	Hydrophobic	false
C5	CD1	TYR- 132	4.13	0	Hydrophobic	false
C15	CB	TYR- 132	4.06	0	Hydrophobic	false
C69	CB	TYR- 132	4.37	0	Hydrophobic	false
C13	CB	THR- 133	4.02	0	Hydrophobic	false
C45	CG2	THR- 133	3.91	0	Hydrophobic	false
O7	N	GLN- 134	3.04	164.62	H-Bond (Protein Donor)	false
C8	CB	GLN- 134	3.81	0	Hydrophobic	false
C33	CD1	ILE- 171	4.03	0	Hydrophobic	false
C5	CD1	ILE- 179	3.82	0	Hydrophobic	false
C56	CD1	ILE- 287	3.8	0	Hydrophobic	false
N20	OD1	ASP- 289	3.9	0	Ionic (Ligand Cationic)	false
N20	OD2	ASP- 289	2.67	0	Ionic (Ligand Cationic)	false
N20	OD2	ASP- 289	2.67	168.64	H-Bond (Ligand Donor)	false
N2	O	GLY- 291	2.85	156.69	H-Bond (Ligand Donor)	false
C8	CB	THR- 292	4.43	0	Hydrophobic	false
C13	CG2	THR- 292	3.95	0	Hydrophobic	false
C11	CB	THR- 293	4.31	0	Hydrophobic	false
O53	N	ASN- 294	2.92	147.09	H-Bond (Protein Donor)	false
C58	CB	THR- 390	4.46	0	Hydrophobic	false
C57	CG2	VAL- 393	4.16	0	Hydrophobic	false