scPDB - 3l5e entry

Protein Data Bank Entry:

PDB ID : 3l5e

Resolution :1.530 Å

Experimental Method : X-ray

Deposition Date : 2009-12-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.570	7.570	7.570	0.000	7.570	1

List of CHEMBLId :

CHEMBL1231280

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:	16.088
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.691	621.000

% Hydrophobic	% Polar
33.15	66.85
According to VolSite

Ligand :

HET Code:	BDW
Formula:	C32H50N5O2
Molecular weight:	536.772 g/mol
DrugBank ID:	-
Buried Surface Area:	54.1 %
Polar Surface area:	90.27 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	5
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
20.5033	33.3234	56.8551

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
C28	CD1	LEU- 91	3.98	0	Hydrophobic	false
C15	CD2	LEU- 91	3.51	0	Hydrophobic	false
N1	OD2	ASP- 93	2.66	155.27	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 93	3.42	124.53	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 93	2.82	168.78	H-Bond (Ligand Donor)	false
C2	OD2	ASP- 93	3.42	0	Ionic (Ligand Cationic)	false
C2	OD1	ASP- 93	3.65	0	Ionic (Ligand Cationic)	false
C19	CB	SER- 96	3.69	0	Hydrophobic	false
C29	CB	SER- 96	3.63	0	Hydrophobic	false
C33	CG1	VAL- 130	3.66	0	Hydrophobic	false
C18	CZ	TYR- 132	3.97	0	Hydrophobic	false
C14	CE1	PHE- 169	4.32	0	Hydrophobic	false
C26	CD1	ILE- 171	3.71	0	Hydrophobic	false
C16	CH2	TRP- 176	4.19	0	Hydrophobic	false
C14	CD1	ILE- 179	4.31	0	Hydrophobic	false
C30	CD1	ILE- 187	4.27	0	Hydrophobic	false
C31	CB	ILE- 187	3.78	0	Hydrophobic	false
C33	CG	ARG- 189	3.91	0	Hydrophobic	false
C30	CE1	TYR- 259	4.17	0	Hydrophobic	false
C2	OD2	ASP- 289	3.89	0	Ionic (Ligand Cationic)	false
N3	OD2	ASP- 289	2.84	155.22	H-Bond (Ligand Donor)	false
C13	CB	THR- 292	4.28	0	Hydrophobic	false
O2	N	THR- 293	2.98	174.83	H-Bond (Protein Donor)	false
N5	OG1	THR- 293	2.81	157.87	H-Bond (Ligand Donor)	false