scPDB - 3udk entry

Protein Data Bank Entry:

PDB ID : 3udk

Resolution :2.510 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:	33.099
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.726	860.625

% Hydrophobic	% Polar
34.12	65.88
According to VolSite

Ligand :

HET Code:	095
Formula:	C17H21N2O4
Molecular weight:	317.360 g/mol
DrugBank ID:	-
Buried Surface Area:	50.68 %
Polar Surface area:	81.24 Å2

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

Mass center Coordinates

X	Y	Z
22.1763	36.4502	42.7671

Binding mode :

What is Poseview ?

2D View
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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
C5	CD2	LEU- 30	3.61	0	Hydrophobic	false
N10	OD2	ASP- 32	3.43	131.39	H-Bond (Ligand Donor)	false
N10	OD1	ASP- 32	2.65	153.26	H-Bond (Ligand Donor)	false
N10	OD2	ASP- 32	3.43	0	Ionic (Ligand Cationic)	false
N10	OD1	ASP- 32	2.65	0	Ionic (Ligand Cationic)	false
C4	CE1	TYR- 71	3.82	0	Hydrophobic	false
N16	O	GLN- 73	3.49	153.85	H-Bond (Ligand Donor)	false
C23	CE1	TYR- 198	3.84	0	Hydrophobic	false
C22	CD1	ILE- 226	3.75	0	Hydrophobic	false
N10	OD1	ASP- 228	3.49	0	Ionic (Ligand Cationic)	false
N10	OD2	ASP- 228	2.97	0	Ionic (Ligand Cationic)	false
N10	OD2	ASP- 228	2.97	154.32	H-Bond (Ligand Donor)	false
C20	CG2	VAL- 332	3.89	0	Hydrophobic	false