scPDB - 2wf3 entry

Protein Data Bank Entry:

PDB ID : 2wf3

Resolution :2.080 Å

Experimental Method : X-ray

Deposition Date : 2009-04-02

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:	16.742
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.690	880.875

% Hydrophobic	% Polar
30.27	69.73
According to VolSite

Ligand :

HET Code:	ZY3
Formula:	C31H41N4O5S
Molecular weight:	581.746 g/mol
DrugBank ID:	-
Buried Surface Area:	63.54 %
Polar Surface area:	132.96 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
30.1847	1.60237	34.6746

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
C20	CD1	LEU- 91	3.62	0	Hydrophobic	false
O4	OD2	ASP- 93	2.64	160.72	H-Bond (Ligand Donor)	false
N4	O	GLY- 95	3.26	138.66	H-Bond (Ligand Donor)	false
C30	CB	SER- 96	3.51	0	Hydrophobic	false
C15	CD1	TYR- 132	4.05	0	Hydrophobic	false
C17	CB	TYR- 132	4.23	0	Hydrophobic	false
C22	CD1	TYR- 132	4.1	0	Hydrophobic	false
C30	CD1	TYR- 132	4.31	0	Hydrophobic	false
C6	CB	THR- 133	4.17	0	Hydrophobic	false
C8	CG2	THR- 133	3.83	0	Hydrophobic	false
O3	N	GLN- 134	3.05	161.6	H-Bond (Protein Donor)	false
C5	CB	GLN- 134	3.75	0	Hydrophobic	false
C1	CD1	ILE- 171	3.7	0	Hydrophobic	false
C15	CD1	ILE- 179	3.71	0	Hydrophobic	false
N4	OD1	ASP- 289	3.97	0	Ionic (Ligand Cationic)	false
N4	OD2	ASP- 289	2.72	0	Ionic (Ligand Cationic)	false
N4	OD2	ASP- 289	2.72	176.9	H-Bond (Ligand Donor)	false
N3	O	GLY- 291	2.97	171.47	H-Bond (Ligand Donor)	false
C5	CB	THR- 292	4.49	0	Hydrophobic	false
C6	CG2	THR- 292	4.14	0	Hydrophobic	false
C11	CB	THR- 293	3.96	0	Hydrophobic	false
O1	N	THR- 293	3.25	120.66	H-Bond (Protein Donor)	false
O1	N	ASN- 294	3	148.88	H-Bond (Protein Donor)	false