scPDB - 3lpi entry

Protein Data Bank Entry:

PDB ID : 3lpi

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2010-02-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.520	8.520	8.520	0.000	8.520	1

List of CHEMBLId :

CHEMBL1097319

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:	15.807
Number of residues:	49
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.903	877.500

% Hydrophobic	% Polar
35.00	65.00
According to VolSite

Ligand :

HET Code:	Z74
Formula:	C34H43F2N4O5S
Molecular weight:	657.791 g/mol
DrugBank ID:	-
Buried Surface Area:	65.35 %
Polar Surface area:	132.01 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
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
20.1335	32.7434	58.0328

Binding mode :

What is Poseview ?

2D View
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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
C25	CD2	LEU- 91	3.7	0	Hydrophobic	false
O5	OD2	ASP- 93	2.63	159.05	H-Bond (Ligand Donor)	false
N4	O	GLY- 95	2.88	163.71	H-Bond (Ligand Donor)	false
C31	CB	SER- 96	4.32	0	Hydrophobic	false
C31	CG1	VAL- 130	4.2	0	Hydrophobic	false
C17	CD1	TYR- 132	4.27	0	Hydrophobic	false
C19	CD1	TYR- 132	3.98	0	Hydrophobic	false
C26	CD1	TYR- 132	3.91	0	Hydrophobic	false
C21	CB	TYR- 132	3.82	0	Hydrophobic	false
O1	OG1	THR- 133	3.37	171.65	H-Bond (Protein Donor)	false
O4	N	THR- 133	3.34	122.9	H-Bond (Protein Donor)	false
C15	CG2	THR- 133	3.95	0	Hydrophobic	false
C5	CB	THR- 133	3.64	0	Hydrophobic	false
O4	N	GLN- 134	3.33	172.89	H-Bond (Protein Donor)	false
C21	CB	GLN- 134	4.17	0	Hydrophobic	false
C11	CG	GLN- 134	3.78	0	Hydrophobic	false
F2	CG	GLN- 134	3.35	0	Hydrophobic	false
C4	CB	GLN- 134	3.7	0	Hydrophobic	false
F2	CD1	PHE- 169	3.31	0	Hydrophobic	false
F1	CD1	ILE- 171	3.53	0	Hydrophobic	false
C11	CD1	ILE- 171	4.1	0	Hydrophobic	false
C13	CD1	ILE- 171	3.87	0	Hydrophobic	false
F1	CZ2	TRP- 176	3.36	0	Hydrophobic	false
C19	CD1	ILE- 179	4.01	0	Hydrophobic	false
C33	CB	ILE- 187	4	0	Hydrophobic	false
C32	CD	ARG- 189	4.21	0	Hydrophobic	false
C27	CE1	TYR- 259	3.51	0	Hydrophobic	false
N4	OD1	ASP- 289	3.77	0	Ionic (Ligand Cationic)	false
N4	OD2	ASP- 289	2.7	0	Ionic (Ligand Cationic)	false
N4	OD2	ASP- 289	2.7	161.18	H-Bond (Ligand Donor)	false
N1	O	GLY- 291	2.98	155.65	H-Bond (Ligand Donor)	false
C3	CB	THR- 292	4.37	0	Hydrophobic	false
C2	CG2	THR- 292	4.26	0	Hydrophobic	false
O3	N	THR- 293	2.88	160.73	H-Bond (Protein Donor)	false
C15	CD	ARG- 296	4.33	0	Hydrophobic	false