scPDB - 3lpk entry

Protein Data Bank Entry:

PDB ID : 3lpk

Resolution :1.930 Å

Experimental Method : X-ray

Deposition Date : 2010-02-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	9.100	9.100	9.100	0.000	9.100	1

List of CHEMBLId :

CHEMBL1097342

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
B	100 %

Ligand binding site composition:

B-Factor:	21.898
Number of residues:	52
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.897	850.500

% Hydrophobic	% Polar
34.92	65.08
According to VolSite

Ligand :

HET Code:	Z76
Formula:	C35H43F2N4O6S
Molecular weight:	685.801 g/mol
DrugBank ID:	-
Buried Surface Area:	66.34 %
Polar Surface area:	141.24 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
20.1335	33.1667	57.9384

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
C20	CD2	LEU- 91	3.79	0	Hydrophobic	false
O3	OD2	ASP- 93	2.65	157.64	H-Bond (Ligand Donor)	false
O3	OD1	ASP- 93	3.48	144.96	H-Bond (Ligand Donor)	false
N3	O	GLY- 95	2.92	165.5	H-Bond (Ligand Donor)	false
C32	CB	SER- 96	4.35	0	Hydrophobic	false
C32	CG1	VAL- 130	3.43	0	Hydrophobic	false
C17	CD1	TYR- 132	4.27	0	Hydrophobic	false
C18	CD1	TYR- 132	3.85	0	Hydrophobic	false
C25	CD1	TYR- 132	3.93	0	Hydrophobic	false
C32	CE1	TYR- 132	3.62	0	Hydrophobic	false
C39	CB	TYR- 132	4.43	0	Hydrophobic	false
C24	CB	TYR- 132	3.77	0	Hydrophobic	false
C5	CB	THR- 133	3.73	0	Hydrophobic	false
C14	CG2	THR- 133	3.87	0	Hydrophobic	false
O7	N	THR- 133	2.83	124.62	H-Bond (Protein Donor)	false
O7	OG1	THR- 133	3.38	157.96	H-Bond (Protein Donor)	false
F2	CG	GLN- 134	3.45	0	Hydrophobic	false
C10	CG	GLN- 134	3.67	0	Hydrophobic	false
C22	CG	GLN- 134	3.57	0	Hydrophobic	false
C23	CB	GLN- 134	3.61	0	Hydrophobic	false
C4	CB	GLN- 134	3.63	0	Hydrophobic	false
O2	N	GLN- 134	3.21	163.64	H-Bond (Protein Donor)	false
F2	CE1	PHE- 169	3.81	0	Hydrophobic	false
F1	CD1	ILE- 171	3.67	0	Hydrophobic	false
C12	CD1	ILE- 171	4.32	0	Hydrophobic	false
C11	CD1	ILE- 171	3.42	0	Hydrophobic	false
F1	CZ2	TRP- 176	3.38	0	Hydrophobic	false
C18	CD1	ILE- 179	4.09	0	Hydrophobic	false
C36	CB	ILE- 187	4.03	0	Hydrophobic	false
C32	CD	ARG- 189	4.43	0	Hydrophobic	false
C37	CD	ARG- 189	4.3	0	Hydrophobic	false
C27	CE1	TYR- 259	3.64	0	Hydrophobic	false
N3	OD1	ASP- 289	3.9	0	Ionic (Ligand Cationic)	false
N3	OD2	ASP- 289	2.71	0	Ionic (Ligand Cationic)	false
N3	OD2	ASP- 289	2.71	164.75	H-Bond (Ligand Donor)	false
N2	O	GLY- 291	2.99	159	H-Bond (Ligand Donor)	false
C3	CB	THR- 292	4.37	0	Hydrophobic	false
C1	CG2	THR- 292	4.26	0	Hydrophobic	false
O1	OG1	THR- 293	2.88	141.71	H-Bond (Protein Donor)	false
O1	N	THR- 293	2.73	156.58	H-Bond (Protein Donor)	false
C34	CB	THR- 293	4.35	0	Hydrophobic	false
C14	CD	ARG- 296	4.09	0	Hydrophobic	false