scPDB - 3udn entry

Protein Data Bank Entry:

PDB ID : 3udn

Resolution :2.190 Å

Experimental Method : X-ray

Deposition Date : 2011-10-28

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:	27.126
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.982	1191.375

% Hydrophobic	% Polar
28.90	71.10
According to VolSite

Ligand :

HET Code:	09B
Formula:	C20H18N3O3
Molecular weight:	348.375 g/mol
DrugBank ID:	-
Buried Surface Area:	57.47 %
Polar Surface area:	95.8 Å2

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

Mass center Coordinates

X	Y	Z
20.9604	37.7108	41.9988

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
C13	CD2	LEU- 30	3.5	0	Hydrophobic	false
N19	OD2	ASP- 32	2.84	143.13	H-Bond (Ligand Donor)	false
N19	OD2	ASP- 32	2.84	0	Ionic (Ligand Cationic)	false
N19	OD1	ASP- 32	3.51	0	Ionic (Ligand Cationic)	false
C5	CB	SER- 35	4.27	0	Hydrophobic	false
C1	CG1	VAL- 69	4.19	0	Hydrophobic	false
C21	CE1	TYR- 71	3.63	0	Hydrophobic	false
C16	CD2	TYR- 71	4.46	0	Hydrophobic	false
C9	CD1	TYR- 71	4.09	0	Hydrophobic	false
N17	O	GLN- 73	2.85	156.75	H-Bond (Ligand Donor)	false
C12	CD1	ILE- 118	4.08	0	Hydrophobic	false
C21	CD1	ILE- 118	4.43	0	Hydrophobic	false
C9	CE1	TYR- 198	4	0	Hydrophobic	false
N19	OD1	ASP- 228	3.75	0	Ionic (Ligand Cationic)	false
N19	OD2	ASP- 228	2.71	0	Ionic (Ligand Cationic)	false
N19	OD2	ASP- 228	2.71	130.25	H-Bond (Ligand Donor)	false