scPDB - 2xfi entry

Protein Data Bank Entry:

PDB ID : 2xfi

Resolution :1.730 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:	23.704
Number of residues:	46
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.005	806.625

% Hydrophobic	% Polar
40.17	59.83
According to VolSite

Ligand :

HET Code:	XFI
Formula:	C33H43N4O5S
Molecular weight:	607.783 g/mol
DrugBank ID:	-
Buried Surface Area:	61.91 %
Polar Surface area:	140.79 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
30.7244	2.39693	34.7285

Binding mode :

What is Poseview ?

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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
C13	CD1	LEU- 91	3.63	0	Hydrophobic	false
O6	OD1	ASP- 93	3.5	138.72	H-Bond (Ligand Donor)	false
O6	OD2	ASP- 93	2.58	165.5	H-Bond (Ligand Donor)	false
N3	O	GLY- 95	3.09	143.55	H-Bond (Ligand Donor)	false
N37	O	GLY- 95	2.94	150.23	H-Bond (Ligand Donor)	false
C39	CB	SER- 96	3.48	0	Hydrophobic	false
C40	CG1	VAL- 130	3.56	0	Hydrophobic	false
C5	CD1	TYR- 132	3.98	0	Hydrophobic	false
C8	CD1	TYR- 132	3.89	0	Hydrophobic	false
C10	CB	TYR- 132	4.22	0	Hydrophobic	false
C39	CD1	TYR- 132	3.8	0	Hydrophobic	false
C1	CG2	THR- 133	3.9	0	Hydrophobic	false
C29	CB	THR- 133	4.08	0	Hydrophobic	false
O17	OG1	THR- 133	2.59	147.57	H-Bond (Protein Donor)	false
O36	N	THR- 133	3.34	137.89	H-Bond (Protein Donor)	false
O17	N	GLN- 134	2.97	146.5	H-Bond (Protein Donor)	false
C26	CB	GLN- 134	3.89	0	Hydrophobic	false
C18	CB	GLN- 134	3.81	0	Hydrophobic	false
C8	CD1	ILE- 179	3.69	0	Hydrophobic	false
C41	CG	ARG- 189	4.28	0	Hydrophobic	false
C43	CZ	TYR- 259	4.22	0	Hydrophobic	false
C1	CD1	ILE- 287	4.27	0	Hydrophobic	false
N3	OD1	ASP- 289	3.83	0	Ionic (Ligand Cationic)	false
N3	OD2	ASP- 289	2.71	0	Ionic (Ligand Cationic)	false
N3	OD2	ASP- 289	2.71	174.32	H-Bond (Ligand Donor)	false
N15	O	GLY- 291	2.78	173.48	H-Bond (Ligand Donor)	false
C18	CB	THR- 292	4.45	0	Hydrophobic	false
C22	CG2	THR- 292	4.2	0	Hydrophobic	false
C21	CB	THR- 293	4.18	0	Hydrophobic	false
O33	N	ASN- 294	2.98	149.68	H-Bond (Protein Donor)	false
C30	CD	ARG- 296	4	0	Hydrophobic	false