scPDB - 3udq entry

Protein Data Bank Entry:

PDB ID : 3udq

Resolution :2.730 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:	34.661
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.682	820.125

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	09E
Formula:	C21H20BrN2O5S
Molecular weight:	492.363 g/mol
DrugBank ID:	-
Buried Surface Area:	59.02 %
Polar Surface area:	114.52 Å2

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

Mass center Coordinates

X	Y	Z
20.642	37.8212	43.0301

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	3.34	0	Hydrophobic	false
N1	OD1	ASP- 32	2.83	167.55	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 32	2.83	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 32	3.3	0	Ionic (Ligand Cationic)	false
BR1	CB	SER- 35	4.22	0	Hydrophobic	false
C2	CD2	TYR- 71	4.32	0	Hydrophobic	false
C4	CZ	TYR- 71	3.94	0	Hydrophobic	false
C13	CD1	TYR- 71	4.31	0	Hydrophobic	false
BR1	CE1	TYR- 71	4.27	0	Hydrophobic	false
O5	N	THR- 72	2.86	138.08	H-Bond (Protein Donor)	false
N2	O	GLN- 73	2.73	155.73	H-Bond (Ligand Donor)	false
C8	CE1	PHE- 108	3.48	0	Hydrophobic	false
C3	CD1	ILE- 118	3.83	0	Hydrophobic	false
BR1	CB	ILE- 126	4.31	0	Hydrophobic	false
C13	CE1	TYR- 198	4.17	0	Hydrophobic	false
N1	OD1	ASP- 228	3.42	122.01	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 228	2.62	160.03	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 228	3.42	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 228	2.62	0	Ionic (Ligand Cationic)	false
C15	CG2	THR- 329	4.33	0	Hydrophobic	false