scPDB - 4dju entry

Protein Data Bank Entry:

PDB ID : 4dju

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2012-02-02

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:	22.864
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.960	968.625

% Hydrophobic	% Polar
33.10	66.90
According to VolSite

Ligand :

HET Code:	0KK
Formula:	C16H16N3O
Molecular weight:	266.318 g/mol
DrugBank ID:	-
Buried Surface Area:	54.2 %
Polar Surface area:	57.93 Å2

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

Mass center Coordinates

X	Y	Z
21.6165	10.9884	21.549

Binding mode :

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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
C15	CD2	LEU- 91	3.61	0	Hydrophobic	false
N1	OD2	ASP- 93	2.66	159	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 93	2.8	169.45	H-Bond (Ligand Donor)	false
C3	OD2	ASP- 93	3.46	0	Ionic (Ligand Cationic)	false
C3	OD1	ASP- 93	3.56	0	Ionic (Ligand Cationic)	false
C7	CB	SER- 96	3.91	0	Hydrophobic	false
C8	CG1	VAL- 130	3.58	0	Hydrophobic	false
C9	CB	TYR- 132	3.79	0	Hydrophobic	false
C6	CD1	ILE- 179	3.61	0	Hydrophobic	false
C16	CD1	ILE- 179	3.87	0	Hydrophobic	false
C3	OD2	ASP- 289	3.87	0	Ionic (Ligand Cationic)	false
N3	OD2	ASP- 289	2.82	156.56	H-Bond (Ligand Donor)	false