scPDB - 4jp9 entry

Protein Data Bank Entry:

PDB ID : 4jp9

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2013-03-19

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:	13.226
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.621	597.375

% Hydrophobic	% Polar
37.85	62.15
According to VolSite

Ligand :

HET Code:	1M5
Formula:	C20H21ClN3O2
Molecular weight:	370.853 g/mol
DrugBank ID:	-
Buried Surface Area:	55.53 %
Polar Surface area:	69.53 Å2

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

Mass center Coordinates

X	Y	Z
25.1803	15.3692	9.05431

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
C21	CD1	LEU- 78	3.89	0	Hydrophobic	false
C16	OD1	ASP- 80	3.61	0	Ionic (Ligand Cationic)	false
C16	OD2	ASP- 80	3.5	0	Ionic (Ligand Cationic)	false
N17	OD2	ASP- 80	2.76	162.91	H-Bond (Ligand Donor)	false
N18	OD1	ASP- 80	2.82	158.17	H-Bond (Ligand Donor)	false
C13	CB	SER- 83	3.96	0	Hydrophobic	false
C12	CG1	VAL- 117	4.49	0	Hydrophobic	false
C12	CD2	TYR- 119	3.87	0	Hydrophobic	false
C8	CE1	PHE- 156	4.45	0	Hydrophobic	false
C24	CD1	ILE- 158	3.57	0	Hydrophobic	false
C13	CD1	ILE- 166	3.69	0	Hydrophobic	false
C3	CD1	ILE- 166	3.23	0	Hydrophobic	false
C16	OD2	ASP- 276	3.88	0	Ionic (Ligand Cationic)	false
N18	OD2	ASP- 276	2.81	159.5	H-Bond (Ligand Donor)	false