scPDB - 3l5d entry

Protein Data Bank Entry:

PDB ID : 3l5d

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2009-12-21

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
B	100 %

Ligand binding site composition:

B-Factor:	16.758
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.981	715.500

% Hydrophobic	% Polar
34.43	65.57
According to VolSite

Ligand :

HET Code:	BDV
Formula:	C21H34N5O2
Molecular weight:	388.527 g/mol
DrugBank ID:	-
Buried Surface Area:	44.38 %
Polar Surface area:	99.06 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
18.7098	32.8631	57.0525

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
C8	CD2	LEU- 91	3.85	0	Hydrophobic	false
C21	CD2	LEU- 91	3.91	0	Hydrophobic	false
N1	OD2	ASP- 93	2.57	153.18	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 93	3.25	125.33	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 93	2.85	167.49	H-Bond (Ligand Donor)	false
C2	OD2	ASP- 93	3.29	0	Ionic (Ligand Cationic)	false
C2	OD1	ASP- 93	3.71	0	Ionic (Ligand Cationic)	false
C4	CB	SER- 96	4.02	0	Hydrophobic	false
C5	CE1	PHE- 169	4.19	0	Hydrophobic	false
C7	CE1	PHE- 169	3.98	0	Hydrophobic	false
C18	CD1	ILE- 171	3.73	0	Hydrophobic	false
C8	CD1	ILE- 179	3.96	0	Hydrophobic	false
C5	CD1	ILE- 179	3.98	0	Hydrophobic	false
N3	OD2	ASP- 289	2.97	157.56	H-Bond (Ligand Donor)	false
C15	CB	THR- 292	4.17	0	Hydrophobic	false
O2	N	THR- 293	2.86	174.93	H-Bond (Protein Donor)	false
N5	OG1	THR- 293	2.71	161.25	H-Bond (Ligand Donor)	false