scPDB - 3zki entry

Protein Data Bank Entry:

PDB ID : 3zki

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2013-01-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-secretase 2
ID:	BACE2_HUMAN
AC:	Q9Y5Z0
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.23.45

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	36.320
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.100	1532.250

% Hydrophobic	% Polar
35.68	64.32
According to VolSite

Ligand :

HET Code:	WZV
Formula:	C20H21F3N5O3
Molecular weight:	436.408 g/mol
DrugBank ID:	-
Buried Surface Area:	58.09 %
Polar Surface area:	111.52 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:	6

Mass center Coordinates

X	Y	Z
-21.6595	-22.165	-7.80071

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
F31	CE2	TYR- 30	3.38	0	Hydrophobic	false
C12	CD2	LEU- 46	4.11	0	Hydrophobic	false
C8	CD2	LEU- 46	4.42	0	Hydrophobic	false
N15	OD1	ASP- 48	3.04	166.32	H-Bond (Ligand Donor)	false
N15	OD2	ASP- 48	3.47	131.04	H-Bond (Ligand Donor)	false
C14	CB	SER- 51	3.97	0	Hydrophobic	false
C2	CD1	TYR- 87	3.61	0	Hydrophobic	false
C14	CZ	TYR- 87	3.45	0	Hydrophobic	false
C14	CD1	ILE- 134	3.94	0	Hydrophobic	false
C10	CD1	ILE- 134	3.82	0	Hydrophobic	false
N15	OD2	ASP- 241	2.88	151.71	H-Bond (Ligand Donor)	false
N13	O	GLY- 243	2.82	162.39	H-Bond (Ligand Donor)	false
F30	CG2	THR- 245	3.66	0	Hydrophobic	false
C18	CB	THR- 245	4.27	0	Hydrophobic	false
F31	CB	ALA- 347	3.39	0	Hydrophobic	false
F30	CG2	THR- 348	3.33	0	Hydrophobic	false
O16	O	HOH- 2019	2.87	158.59	H-Bond (Protein Donor)	false