scPDB - 3duy entry

Protein Data Bank Entry:

PDB ID : 3duy

Resolution :1.970 Å

Experimental Method : X-ray

Deposition Date : 2008-07-18

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
B	100 %

Ligand binding site composition:

B-Factor:	27.075
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.066	887.625

% Hydrophobic	% Polar
36.50	63.50
According to VolSite

Ligand :

HET Code:	AFJ
Formula:	C25H49N3O4S
Molecular weight:	487.739 g/mol
DrugBank ID:	-
Buried Surface Area:	64.25 %
Polar Surface area:	132.82 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
16.9188	6.37152	-19.7618

Binding mode :

What is Poseview ?

2D View
3D View

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
C22	CD1	LEU- 30	3.87	0	Hydrophobic	false
C75	CD2	LEU- 30	3.85	0	Hydrophobic	false
N51	O	GLY- 34	2.91	176.69	H-Bond (Ligand Donor)	false
C56	CB	SER- 35	4.06	0	Hydrophobic	false
C62	CG1	VAL- 69	3.8	0	Hydrophobic	false
C36	CD1	TYR- 71	4.05	0	Hydrophobic	false
C66	CD1	TYR- 71	4.2	0	Hydrophobic	false
C71	CG	TYR- 71	3.74	0	Hydrophobic	false
C5	CG2	THR- 72	3.87	0	Hydrophobic	false
S1	CG2	THR- 72	3.78	0	Hydrophobic	false
O50	N	THR- 72	2.99	143.03	H-Bond (Protein Donor)	false
C5	CG	GLN- 73	3.9	0	Hydrophobic	false
S1	CG	GLN- 73	3.91	0	Hydrophobic	false
O31	N	GLN- 73	2.99	164.72	H-Bond (Protein Donor)	false
C71	CD1	PHE- 108	3.77	0	Hydrophobic	false
C75	CE1	PHE- 108	4.16	0	Hydrophobic	false
C26	CG1	ILE- 110	4.08	0	Hydrophobic	false
C26	CZ2	TRP- 115	4.07	0	Hydrophobic	false
C75	CH2	TRP- 115	4.14	0	Hydrophobic	false
C66	CD1	ILE- 118	4.33	0	Hydrophobic	false
C75	CD1	ILE- 118	4.23	0	Hydrophobic	false
C56	CD1	ILE- 126	4.36	0	Hydrophobic	false
C62	CG	ARG- 128	4.19	0	Hydrophobic	false
C45	CE1	TYR- 198	4.45	0	Hydrophobic	false
C56	CE1	TYR- 198	4.23	0	Hydrophobic	false
C45	CD1	ILE- 226	3.95	0	Hydrophobic	false
O38	OD2	ASP- 228	2.61	172.16	H-Bond (Ligand Donor)	false
N32	O	GLY- 230	3.08	164.51	H-Bond (Ligand Donor)	false
C2	CG2	THR- 231	4.33	0	Hydrophobic	false
O13	N	THR- 232	2.87	167.9	H-Bond (Protein Donor)	false
S1	CD	ARG- 235	4.06	0	Hydrophobic	false