scPDB - 4azy entry

Protein Data Bank Entry:

PDB ID : 4azy

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2012-06-27

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:	19.356
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.124	1073.250

% Hydrophobic	% Polar
38.05	61.95
According to VolSite

Ligand :

HET Code:	7F3
Formula:	C24H15F5N5
Molecular weight:	468.401 g/mol
DrugBank ID:	-
Buried Surface Area:	63.36 %
Polar Surface area:	78.66 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
5.42738	1.67282	-21.0138

Binding mode :

What is Poseview ?

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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
C17	CD1	LEU- 30	4.13	0	Hydrophobic	false
C8	OD1	ASP- 32	3.62	0	Ionic (Ligand Cationic)	false
C8	OD2	ASP- 32	3.44	0	Ionic (Ligand Cationic)	false
N9	OD2	ASP- 32	2.68	160.4	H-Bond (Ligand Donor)	false
N34	OD1	ASP- 32	2.81	171.39	H-Bond (Ligand Donor)	false
N34	OD2	ASP- 32	3.48	122.64	H-Bond (Ligand Donor)	false
C29	CB	SER- 35	4.06	0	Hydrophobic	false
F32	CB	SER- 35	3.63	0	Hydrophobic	false
F33	CB	ASN- 37	3.52	0	Hydrophobic	false
F31	CB	ALA- 39	3.52	0	Hydrophobic	false
N27	NE1	TRP- 76	3.01	151.79	H-Bond (Protein Donor)	false
F33	CZ2	TRP- 76	3.98	0	Hydrophobic	false
F31	CE2	TRP- 76	3.54	0	Hydrophobic	false
F31	CE1	PHE- 108	3.53	0	Hydrophobic	false
F23	CD1	ILE- 110	3.51	0	Hydrophobic	false
F23	CZ2	TRP- 115	3.23	0	Hydrophobic	false
C29	CD1	ILE- 118	3.81	0	Hydrophobic	false
F31	CB	ILE- 118	4.32	0	Hydrophobic	false
F32	CG2	ILE- 118	3.45	0	Hydrophobic	false
C12	CD1	ILE- 118	3.51	0	Hydrophobic	false
N34	OD2	ASP- 228	2.91	155.06	H-Bond (Ligand Donor)	false
F7	CB	THR- 231	4.31	0	Hydrophobic	false