scPDB - 3n4l entry

Protein Data Bank Entry:

PDB ID : 3n4l

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2010-05-21

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
B	100 %

Ligand binding site composition:

B-Factor:	58.960
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.556	482.625

% Hydrophobic	% Polar
34.97	65.03
According to VolSite

Ligand :

HET Code:	842
Formula:	C27H33F2N4O2
Molecular weight:	483.573 g/mol
DrugBank ID:	-
Buried Surface Area:	62.14 %
Polar Surface area:	83.76 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
66.8433	-42.7996	22.2975

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
F34	CD1	LEU- 36	3.47	0	Hydrophobic	false
O35	OD1	ASP- 38	2.79	165.12	H-Bond (Ligand Donor)	false
N7	O	GLY- 40	3.07	141.91	H-Bond (Ligand Donor)	false
C5	CD1	TYR- 77	4.47	0	Hydrophobic	false
C26	CD1	TYR- 77	4.33	0	Hydrophobic	false
F33	CD2	TYR- 77	3.7	0	Hydrophobic	false
C28	CB	TYR- 77	3.67	0	Hydrophobic	false
C1	CG2	THR- 78	4.22	0	Hydrophobic	false
C13	CG2	THR- 78	3.84	0	Hydrophobic	false
C19	CG2	THR- 78	3.43	0	Hydrophobic	false
O25	N	THR- 78	3.1	155.96	H-Bond (Protein Donor)	false
F33	CE1	PHE- 114	3.46	0	Hydrophobic	false
F34	CD1	ILE- 116	4.23	0	Hydrophobic	false
F34	CZ2	TRP- 121	3.31	0	Hydrophobic	false
C26	CD1	ILE- 124	4.02	0	Hydrophobic	false
N21	OH	TYR- 204	2.68	159.96	H-Bond (Protein Donor)	false
C9	CE1	TYR- 204	3.62	0	Hydrophobic	false
C10	CD1	ILE- 232	3.51	0	Hydrophobic	false
N7	OD1	ASP- 234	3.64	0	Ionic (Ligand Cationic)	false
N7	OD2	ASP- 234	3.14	0	Ionic (Ligand Cationic)	false
N7	OD2	ASP- 234	3.14	128.09	H-Bond (Ligand Donor)	false
N3	O	GLY- 236	3.41	124.37	H-Bond (Ligand Donor)	false
C11	CG2	VAL- 338	4.02	0	Hydrophobic	false