scPDB - 2f3f entry

Protein Data Bank Entry:

PDB ID : 2f3f

Resolution :2.300 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	100 %

Ligand binding site composition:

B-Factor:	43.419
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.746	749.250

% Hydrophobic	% Polar
28.83	71.17
According to VolSite

Ligand :

HET Code:	AXF
Formula:	C24H43N4O4S2
Molecular weight:	515.753 g/mol
DrugBank ID:	-
Buried Surface Area:	67.23 %
Polar Surface area:	174.74 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
30.8081	6.16397	15.0638

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
C14	CD2	LEU- 30	4.47	0	Hydrophobic	false
S30	CD2	LEU- 30	3.77	0	Hydrophobic	false
N56	O	GLY- 34	2.76	167.49	H-Bond (Ligand Donor)	false
C61	CB	SER- 35	3.96	0	Hydrophobic	false
C67	CG1	VAL- 69	3.87	0	Hydrophobic	false
C27	CD1	TYR- 71	3.91	0	Hydrophobic	false
C31	CD2	TYR- 71	3.65	0	Hydrophobic	false
C41	CD1	TYR- 71	4	0	Hydrophobic	false
C45	CB	THR- 72	4.41	0	Hydrophobic	false
C72	CB	THR- 72	4.16	0	Hydrophobic	false
O55	N	THR- 72	3.09	145.15	H-Bond (Protein Donor)	false
O71	N	GLN- 73	3.2	157.58	H-Bond (Protein Donor)	false
C72	CB	GLN- 73	3.8	0	Hydrophobic	false
C31	CE1	PHE- 108	3.85	0	Hydrophobic	false
C38	CD1	ILE- 110	3.98	0	Hydrophobic	false
C11	CG1	ILE- 110	4.18	0	Hydrophobic	false
C14	CZ2	TRP- 115	3.99	0	Hydrophobic	false
C27	CD1	ILE- 118	4.04	0	Hydrophobic	false
C61	CD1	ILE- 126	4.12	0	Hydrophobic	false
C64	CB	ILE- 126	4.28	0	Hydrophobic	false
C67	CG	ARG- 128	4.23	0	Hydrophobic	false
C50	CE1	TYR- 198	4.16	0	Hydrophobic	false
C61	CE1	TYR- 198	4.15	0	Hydrophobic	false
C50	CD1	ILE- 226	3.89	0	Hydrophobic	false
N23	O	GLY- 230	3.16	169.78	H-Bond (Ligand Donor)	false
N6	OG1	THR- 232	2.97	157.28	H-Bond (Ligand Donor)	false
O76	N	THR- 232	3.2	160.96	H-Bond (Protein Donor)	false