scPDB - 4j1c entry

Protein Data Bank Entry:

PDB ID : 4j1c

Resolution :2.010 Å

Experimental Method : X-ray

Deposition Date : 2013-02-01

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:	41.038
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.538	705.375

% Hydrophobic	% Polar
32.06	67.94
According to VolSite

Ligand :

HET Code:	1HO
Formula:	C18H14F4N5O2
Molecular weight:	408.330 g/mol
DrugBank ID:	-
Buried Surface Area:	62.74 %
Polar Surface area:	115 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-18.8238	-40.8312	-6.46159

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
C15	CD2	LEU- 91	4.05	0	Hydrophobic	false
C13	CD2	LEU- 91	4.22	0	Hydrophobic	false
N7	OD1	ASP- 93	2.78	164.41	H-Bond (Ligand Donor)	false
N7	OD2	ASP- 93	3.43	125.94	H-Bond (Ligand Donor)	false
F10	CB	SER- 96	3.25	0	Hydrophobic	false
C9	CZ	TYR- 132	3.61	0	Hydrophobic	false
F10	CE1	TYR- 132	3.43	0	Hydrophobic	false
F11	CG	TYR- 132	3.58	0	Hydrophobic	false
F18	CZ	TYR- 132	3.54	0	Hydrophobic	false
F12	CD1	TYR- 132	3.49	0	Hydrophobic	false
F18	CE1	PHE- 169	3.21	0	Hydrophobic	false
C9	CD1	ILE- 179	3.45	0	Hydrophobic	false
C17	CD1	ILE- 179	4.12	0	Hydrophobic	false
N7	OD2	ASP- 289	2.76	159.81	H-Bond (Ligand Donor)	false
N19	O	GLY- 291	2.89	139.6	H-Bond (Ligand Donor)	false
N29	OG1	THR- 293	3.5	159.69	H-Bond (Protein Donor)	false
C25	CB	THR- 293	4.38	0	Hydrophobic	false