scPDB - 2f3e entry

Protein Data Bank Entry:

PDB ID : 2f3e

Resolution :2.110 Å

Experimental Method : X-ray

Deposition Date : 2005-11-21

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	98 %
B	2 %

Ligand binding site composition:

B-Factor:	46.581
Number of residues:	47
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.787	799.875

% Hydrophobic	% Polar
29.96	70.04
According to VolSite

Ligand :

HET Code:	AXQ
Formula:	C31H55N5O7S2
Molecular weight:	673.928 g/mol
DrugBank ID:	-
Buried Surface Area:	57.34 %
Polar Surface area:	225.55 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	6
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
29.5089	5.60609	14.9679

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
C21	CD1	LEU- 30	4.06	0	Hydrophobic	false
C28	CD2	LEU- 30	3.35	0	Hydrophobic	false
O57	OD1	ASP- 32	2.54	134.23	H-Bond (Protein Donor)	false
N70	O	GLY- 34	2.85	168.89	H-Bond (Ligand Donor)	false
C74	CB	SER- 35	3.89	0	Hydrophobic	false
C80	CG1	VAL- 69	4	0	Hydrophobic	false
N86	O	PRO- 70	2.96	161.29	H-Bond (Ligand Donor)	false
C91	CG	PRO- 70	3.96	0	Hydrophobic	false
C97	CB	PRO- 70	4.42	0	Hydrophobic	false
S1	CG	TYR- 71	4.22	0	Hydrophobic	false
C2	CD1	TYR- 71	4.12	0	Hydrophobic	false
C55	CD1	TYR- 71	3.98	0	Hydrophobic	false
C74	CD1	TYR- 71	4.5	0	Hydrophobic	false
C50	CB	THR- 72	3.62	0	Hydrophobic	false
C59	CB	THR- 72	4.48	0	Hydrophobic	false
O69	OG1	THR- 72	3.47	164.65	H-Bond (Protein Donor)	false
O69	N	THR- 72	3.04	143.98	H-Bond (Protein Donor)	false
O34	NE2	GLN- 73	3.26	131.04	H-Bond (Protein Donor)	false
O54	N	GLN- 73	3.07	137.67	H-Bond (Protein Donor)	false
C50	CG	GLN- 73	3.91	0	Hydrophobic	false
C28	CE1	PHE- 108	4.24	0	Hydrophobic	false
S20	CD1	ILE- 110	3.55	0	Hydrophobic	false
C21	CZ2	TRP- 115	4.38	0	Hydrophobic	false
C28	CH2	TRP- 115	4.18	0	Hydrophobic	false
C2	CD1	ILE- 118	4.32	0	Hydrophobic	false
C76	CD1	ILE- 126	3.72	0	Hydrophobic	false
C64	CE1	TYR- 198	4.26	0	Hydrophobic	false
C76	CE1	TYR- 198	3.75	0	Hydrophobic	false
O85	OH	TYR- 198	2.5	173.54	H-Bond (Protein Donor)	false
C64	CD1	ILE- 226	3.96	0	Hydrophobic	false
O57	OD2	ASP- 228	2.68	169.34	H-Bond (Ligand Donor)	false
N7	O	GLY- 230	3.09	167.67	H-Bond (Ligand Donor)	false
N31	OG1	THR- 232	2.82	139.02	H-Bond (Ligand Donor)	false
O49	N	THR- 232	3.01	170.95	H-Bond (Protein Donor)	false