scPDB - 3zmg entry

Protein Data Bank Entry:

PDB ID : 3zmg

Resolution :1.740 Å

Experimental Method : X-ray

Deposition Date : 2013-02-08

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:	21.985
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.857	779.625

% Hydrophobic	% Polar
35.50	64.50
According to VolSite

Ligand :

HET Code:	6Z0
Formula:	C18H15F3N5O2
Molecular weight:	390.339 g/mol
DrugBank ID:	-
Buried Surface Area:	60.62 %
Polar Surface area:	112.63 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-18.5258	41.0141	6.62679

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
C13	CD2	LEU- 91	4.16	0	Hydrophobic	false
C17	CD2	LEU- 91	4.35	0	Hydrophobic	false
N24	OD2	ASP- 93	3.42	126.3	H-Bond (Ligand Donor)	false
N24	OD1	ASP- 93	2.85	162.39	H-Bond (Ligand Donor)	false
C20	CB	SER- 96	4.15	0	Hydrophobic	false
F18	CZ	TYR- 132	3.28	0	Hydrophobic	false
C20	CE1	TYR- 132	3.6	0	Hydrophobic	false
F27	CD1	TYR- 132	3.45	0	Hydrophobic	false
F18	CE1	PHE- 169	3.31	0	Hydrophobic	false
C20	CD1	ILE- 179	3.72	0	Hydrophobic	false
C15	CD1	ILE- 179	3.95	0	Hydrophobic	false
N24	OD2	ASP- 289	2.89	162.71	H-Bond (Ligand Donor)	false
N9	O	GLY- 291	3.01	133.63	H-Bond (Ligand Donor)	false
C1	CB	THR- 293	4.42	0	Hydrophobic	false