scPDB - 3r2f entry

Protein Data Bank Entry:

PDB ID : 3r2f

Resolution :2.530 Å

Experimental Method : X-ray

Deposition Date : 2011-03-14

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
E	100 %

Ligand binding site composition:

B-Factor:	21.029
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.886	914.625

% Hydrophobic	% Polar
27.31	72.69
According to VolSite

Ligand :

HET Code:	PB0
Formula:	C36H51F2N4O5
Molecular weight:	657.811 g/mol
DrugBank ID:	-
Buried Surface Area:	59.74 %
Polar Surface area:	124.58 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
35.5327	18.2974	72.8584

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
C25	CD1	LEU- 30	3.95	0	Hydrophobic	false
F47	CD2	LEU- 30	3.35	0	Hydrophobic	false
O44	OD1	ASP- 32	3.2	175.24	H-Bond (Ligand Donor)	false
N37	O	GLY- 34	2.96	162.41	H-Bond (Ligand Donor)	false
C30	CB	SER- 35	4.38	0	Hydrophobic	false
C17	CB	TYR- 71	4.07	0	Hydrophobic	false
C28	CD1	TYR- 71	3.67	0	Hydrophobic	false
C30	CD1	TYR- 71	4.22	0	Hydrophobic	false
C34	CD1	TYR- 71	4.33	0	Hydrophobic	false
F46	CD2	TYR- 71	3.78	0	Hydrophobic	false
C6	CB	TYR- 71	3.34	0	Hydrophobic	false
C17	CB	THR- 72	4.37	0	Hydrophobic	false
C31	CB	THR- 72	4.01	0	Hydrophobic	false
C4	CG2	THR- 72	3.63	0	Hydrophobic	false
O43	N	THR- 72	3.24	133.73	H-Bond (Protein Donor)	false
C31	CB	GLN- 73	4.14	0	Hydrophobic	false
C5	CB	GLN- 73	3.87	0	Hydrophobic	false
F46	CD1	PHE- 108	3.48	0	Hydrophobic	false
C26	CG1	ILE- 110	4.26	0	Hydrophobic	false
C35	CD1	ILE- 110	4.34	0	Hydrophobic	false
F47	CD1	ILE- 110	4.35	0	Hydrophobic	false
F47	CH2	TRP- 115	3.4	0	Hydrophobic	false
C28	CD1	ILE- 118	4.34	0	Hydrophobic	false
C24	CD1	ILE- 126	3.78	0	Hydrophobic	false
C20	CE1	TYR- 198	4.35	0	Hydrophobic	false
C24	CE1	TYR- 198	3.76	0	Hydrophobic	false
C32	CE1	TYR- 198	4.39	0	Hydrophobic	false
O45	OH	TYR- 198	3.4	154.35	H-Bond (Protein Donor)	false
N37	OD1	ASP- 228	4	0	Ionic (Ligand Cationic)	false
N37	OD2	ASP- 228	2.79	0	Ionic (Ligand Cationic)	false
N37	OD2	ASP- 228	2.79	166.11	H-Bond (Ligand Donor)	false
N40	O	GLY- 230	2.99	156.23	H-Bond (Ligand Donor)	false
C23	CB	THR- 232	3.94	0	Hydrophobic	false
O41	N	THR- 232	2.98	165.63	H-Bond (Protein Donor)	false
C4	CD	ARG- 235	4.41	0	Hydrophobic	false