scPDB - 2b8v entry

Protein Data Bank Entry:

PDB ID : 2b8v

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2005-10-10

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:	18.101
Number of residues:	45
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.627	398.250

% Hydrophobic	% Polar
37.29	62.71
According to VolSite

Ligand :

HET Code:	3BN
Formula:	C29H34N3O5S
Molecular weight:	536.662 g/mol
DrugBank ID:	-
Buried Surface Area:	68.07 %
Polar Surface area:	128.77 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
30.6538	41.5399	1.86468

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
C20	CB	GLN- 12	4.33	0	Hydrophobic	false
C19	CD1	LEU- 30	3.72	0	Hydrophobic	false
C28	CD2	LEU- 30	3.21	0	Hydrophobic	false
O3	OD1	ASP- 32	3.49	137.87	H-Bond (Ligand Donor)	false
O3	OD2	ASP- 32	2.66	166.31	H-Bond (Ligand Donor)	false
N1	O	GLY- 34	3.2	142.47	H-Bond (Ligand Donor)	false
C5	CD1	TYR- 71	4.09	0	Hydrophobic	false
C8	CD1	TYR- 71	3.76	0	Hydrophobic	false
C24	CB	TYR- 71	3.73	0	Hydrophobic	false
C14	CB	THR- 72	4.15	0	Hydrophobic	false
C16	CG2	THR- 72	3.72	0	Hydrophobic	false
O2	N	GLN- 73	3.13	142.45	H-Bond (Protein Donor)	false
O4	NE2	GLN- 73	3.46	137.01	H-Bond (Protein Donor)	false
C9	CB	GLN- 73	3.93	0	Hydrophobic	false
C25	CD1	PHE- 108	3.5	0	Hydrophobic	false
C21	CD1	ILE- 110	3.25	0	Hydrophobic	false
C8	CD1	ILE- 118	3.86	0	Hydrophobic	false
C3	CE1	TYR- 198	3.42	0	Hydrophobic	false
C3	CD1	ILE- 226	3.27	0	Hydrophobic	false
N1	OD2	ASP- 228	2.67	141.5	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 228	2.67	0	Ionic (Ligand Cationic)	false
N1	OD1	ASP- 228	4	0	Ionic (Ligand Cationic)	false
N2	O	GLY- 230	2.99	176.06	H-Bond (Ligand Donor)	false
C13	CG2	THR- 231	4.01	0	Hydrophobic	false
C12	CB	THR- 232	4.32	0	Hydrophobic	false
O6	N	ASN- 233	2.96	168.24	H-Bond (Protein Donor)	false
C16	CD	ARG- 235	3.97	0	Hydrophobic	false