scPDB - 3pi5 entry

Protein Data Bank Entry:

PDB ID : 3pi5

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2010-11-05

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
C	100 %

Ligand binding site composition:

B-Factor:	46.058
Number of residues:	38
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.698	739.125

% Hydrophobic	% Polar
26.48	73.52
According to VolSite

Ligand :

HET Code:	3P5
Formula:	C22H26BrNO4S
Molecular weight:	480.415 g/mol
DrugBank ID:	-
Buried Surface Area:	62.37 %
Polar Surface area:	95.01 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
9.77666	-43.2807	48.7362

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
C2	CD2	LEU- 30	3.81	0	Hydrophobic	false
C9	CD2	LEU- 30	3.5	0	Hydrophobic	false
O52	OD1	ASP- 32	3.42	146.01	H-Bond (Ligand Donor)	false
O52	OD2	ASP- 32	2.53	154.2	H-Bond (Ligand Donor)	false
N29	O	GLY- 34	2.99	146.69	H-Bond (Ligand Donor)	false
C49	CB	SER- 35	3.34	0	Hydrophobic	false
C49	CG1	VAL- 69	3.98	0	Hydrophobic	false
C44	CD1	TYR- 71	4.49	0	Hydrophobic	false
C49	CE1	TYR- 71	3.71	0	Hydrophobic	false
C14	CD1	TYR- 71	3.72	0	Hydrophobic	false
C20	CB	THR- 72	4.43	0	Hydrophobic	false
C42	CB	THR- 72	4.24	0	Hydrophobic	false
O28	N	THR- 72	2.94	124.52	H-Bond (Protein Donor)	false
O27	NE2	GLN- 73	3.08	128.97	H-Bond (Protein Donor)	false
O28	N	GLN- 73	3.45	153.22	H-Bond (Protein Donor)	false
O54	O	PHE- 108	2.65	154.91	H-Bond (Ligand Donor)	false
C4	CE1	PHE- 108	3.42	0	Hydrophobic	false
BR1	CD1	ILE- 110	3.57	0	Hydrophobic	false
BR1	CZ2	TRP- 115	4.07	0	Hydrophobic	false
C11	CD1	ILE- 118	3.9	0	Hydrophobic	false
C46	CD1	ILE- 126	4.15	0	Hydrophobic	false
N29	OD1	ASP- 228	3.96	0	Ionic (Ligand Cationic)	false
N29	OD2	ASP- 228	2.59	0	Ionic (Ligand Cationic)	false
N29	OD2	ASP- 228	2.59	172.48	H-Bond (Ligand Donor)	false
C20	CB	THR- 231	4.49	0	Hydrophobic	false