scPDB - 4j1f entry

Protein Data Bank Entry:

PDB ID : 4j1f

Resolution :2.250 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:	39.410
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.672	870.750

% Hydrophobic	% Polar
31.78	68.22
According to VolSite

Ligand :

HET Code:	1HL
Formula:	C19H16F4N5O2
Molecular weight:	422.356 g/mol
DrugBank ID:	-
Buried Surface Area:	58.4 %
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
-18.0789	-41.672	-6.87993

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
C8	CD2	LEU- 91	4.27	0	Hydrophobic	false
C10	CD2	LEU- 91	4.46	0	Hydrophobic	false
N14	OD2	ASP- 93	3.37	124.87	H-Bond (Ligand Donor)	false
N14	OD1	ASP- 93	2.7	157.75	H-Bond (Ligand Donor)	false
C15	CB	SER- 96	3.99	0	Hydrophobic	false
C2	CD1	TYR- 132	3.89	0	Hydrophobic	false
F13	CD2	TYR- 132	3.25	0	Hydrophobic	false
C15	CZ	TYR- 132	3.47	0	Hydrophobic	false
F29	CB	TYR- 132	3.76	0	Hydrophobic	false
F30	CD1	TYR- 132	3.79	0	Hydrophobic	false
F13	CE1	PHE- 169	3.23	0	Hydrophobic	false
C15	CD1	ILE- 179	4.08	0	Hydrophobic	false
C7	CD1	ILE- 179	3.84	0	Hydrophobic	false
C11	CD1	ILE- 179	4.13	0	Hydrophobic	false
C7	CD1	ILE- 179	3.84	0	Hydrophobic	false
N14	OD2	ASP- 289	2.82	159.11	H-Bond (Ligand Donor)	false
N16	O	GLY- 291	2.95	140.24	H-Bond (Ligand Donor)	false