scPDB - 2zjn entry

Protein Data Bank Entry:

PDB ID : 2zjn

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2008-03-07

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:	35.654
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.526	283.500

% Hydrophobic	% Polar
41.67	58.33
According to VolSite

Ligand :

HET Code:	F1N
Formula:	C25H35ClN3O6S
Molecular weight:	541.080 g/mol
DrugBank ID:	-
Buried Surface Area:	57.78 %
Polar Surface area:	129.77 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
74.6676	35.8203	20.1798

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
CL36	CB	LEU- 30	3.84	0	Hydrophobic	false
C32	CD1	LEU- 30	4.17	0	Hydrophobic	false
C26	CD1	LEU- 30	3.94	0	Hydrophobic	false
CL36	CB	ASP- 32	3.93	0	Hydrophobic	false
C25	CB	ASP- 32	4.02	0	Hydrophobic	false
N20	OD2	ASP- 32	3.05	130.65	H-Bond (Ligand Donor)	false
N20	OD2	ASP- 32	3.05	0	Ionic (Ligand Cationic)	false
C22	CB	SER- 35	3.89	0	Hydrophobic	false
C22	CE1	TYR- 71	4.43	0	Hydrophobic	false
C33	CD2	TYR- 71	4.22	0	Hydrophobic	false
C33	CD1	PHE- 108	4.21	0	Hydrophobic	false
C32	CE1	PHE- 108	3.65	0	Hydrophobic	false
C35	CD1	ILE- 110	3.66	0	Hydrophobic	false
C35	CZ2	TRP- 115	4.4	0	Hydrophobic	false
C32	CH2	TRP- 115	3.85	0	Hydrophobic	false
C25	CD1	ILE- 118	3.93	0	Hydrophobic	false
C3	CE1	TYR- 198	3.72	0	Hydrophobic	false
C3	CD1	ILE- 226	3.37	0	Hydrophobic	false
C6	CD1	ILE- 226	3.95	0	Hydrophobic	false
N4	OD2	ASP- 228	2.87	152.46	H-Bond (Ligand Donor)	false
O15	N	SER- 328	2.75	142.77	H-Bond (Protein Donor)	false
O15	OG	SER- 328	2.92	124.77	H-Bond (Protein Donor)	false
N14	OG	SER- 328	3.23	150.54	H-Bond (Ligand Donor)	false
C10	CG2	THR- 329	3.63	0	Hydrophobic	false
C8	CG2	VAL- 332	3.89	0	Hydrophobic	false