scPDB - 2xfk entry

Protein Data Bank Entry:

PDB ID : 2xfk

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2010-05-24

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:	16.384
Number of residues:	49
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.108	317.250

% Hydrophobic	% Polar
26.60	73.40
According to VolSite

Ligand :

HET Code:	AA9
Formula:	C35H48N5O5S
Molecular weight:	650.851 g/mol
DrugBank ID:	-
Buried Surface Area:	65.79 %
Polar Surface area:	152.82 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
30.3749	1.96346	34.6762

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
C19	CD1	LEU- 91	3.57	0	Hydrophobic	false
O22	OD2	ASP- 93	2.65	160.32	H-Bond (Ligand Donor)	false
O22	OD1	ASP- 93	3.46	142.72	H-Bond (Ligand Donor)	false
N24	O	GLY- 95	3.09	143.31	H-Bond (Ligand Donor)	false
N29	O	GLY- 95	2.92	143.76	H-Bond (Ligand Donor)	false
C31	CB	SER- 96	3.51	0	Hydrophobic	false
C32	CG1	VAL- 130	3.57	0	Hydrophobic	false
C14	CD1	TYR- 132	3.87	0	Hydrophobic	false
C16	CB	TYR- 132	4.17	0	Hydrophobic	false
C21	CD1	TYR- 132	3.98	0	Hydrophobic	false
C31	CD1	TYR- 132	3.77	0	Hydrophobic	false
O11	OG1	THR- 133	2.71	130.65	H-Bond (Protein Donor)	false
O28	N	THR- 133	3.3	138.84	H-Bond (Protein Donor)	false
C26	CG2	THR- 133	3.99	0	Hydrophobic	false
C39	CB	THR- 133	3.89	0	Hydrophobic	false
O11	N	GLN- 134	2.95	146.26	H-Bond (Protein Donor)	false
C42	CB	GLN- 134	3.92	0	Hydrophobic	false
C8	CB	GLN- 134	3.76	0	Hydrophobic	false
C2	CD1	ILE- 171	3.98	0	Hydrophobic	false
C18	CD1	ILE- 171	4.32	0	Hydrophobic	false
C14	CD1	ILE- 179	3.67	0	Hydrophobic	false
C33	CG	ARG- 189	4.41	0	Hydrophobic	false
C35	CZ	TYR- 259	4.25	0	Hydrophobic	false
C26	CD1	ILE- 287	4.1	0	Hydrophobic	false
N24	OD1	ASP- 289	3.82	0	Ionic (Ligand Cationic)	false
N24	OD2	ASP- 289	2.65	0	Ionic (Ligand Cationic)	false
N24	OD2	ASP- 289	2.65	177.45	H-Bond (Ligand Donor)	false
N12	O	GLY- 291	2.77	177.23	H-Bond (Ligand Donor)	false
C8	CB	THR- 292	4.5	0	Hydrophobic	false
C7	CG2	THR- 292	4.19	0	Hydrophobic	false
C5	CB	THR- 293	4.3	0	Hydrophobic	false
O45	N	ASN- 294	2.96	149.42	H-Bond (Protein Donor)	false
C38	CD	ARG- 296	4.01	0	Hydrophobic	false