scPDB - 4ke0 entry

Protein Data Bank Entry:

PDB ID : 4ke0

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2013-04-25

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:	46.778
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.786	546.750

% Hydrophobic	% Polar
36.42	63.58
According to VolSite

Ligand :

HET Code:	1R8
Formula:	C31H43N2O3
Molecular weight:	491.685 g/mol
DrugBank ID:	-
Buried Surface Area:	64.2 %
Polar Surface area:	75.17 Å2

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

Mass center Coordinates

X	Y	Z
30.4709	5.90222	13.612

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
C25	CD1	LEU- 30	4.05	0	Hydrophobic	false
O8	OD1	ASP- 32	3.39	137.74	H-Bond (Ligand Donor)	false
O8	OD2	ASP- 32	2.64	164.72	H-Bond (Ligand Donor)	false
N10	O	GLY- 34	3.09	150.09	H-Bond (Ligand Donor)	false
C21	CB	SER- 35	3.93	0	Hydrophobic	false
C20	CG1	VAL- 69	3.98	0	Hydrophobic	false
C20	CD2	TYR- 71	3.84	0	Hydrophobic	false
C6	CD2	TYR- 71	4.18	0	Hydrophobic	false
C22	CD2	TYR- 71	4.02	0	Hydrophobic	false
C28	CB	TYR- 71	4.42	0	Hydrophobic	false
C36	CB	THR- 72	4.48	0	Hydrophobic	false
C1	CG2	THR- 72	4	0	Hydrophobic	false
C15	CG2	THR- 72	3.83	0	Hydrophobic	false
O32	OG1	THR- 72	2.64	166.47	H-Bond (Protein Donor)	false
O32	N	THR- 72	3.15	154.78	H-Bond (Protein Donor)	false
C26	CD1	ILE- 110	4.27	0	Hydrophobic	false
C30	CD1	ILE- 110	3.69	0	Hydrophobic	false
C29	CZ2	TRP- 115	4.28	0	Hydrophobic	false
C28	CD1	ILE- 118	3.91	0	Hydrophobic	false
C21	CD1	ILE- 126	4.49	0	Hydrophobic	false
C2	CZ	TYR- 198	3.81	0	Hydrophobic	false
C12	CD1	ILE- 226	4.13	0	Hydrophobic	false
C2	CD1	ILE- 226	3.89	0	Hydrophobic	false
N10	OD2	ASP- 228	2.65	171.88	H-Bond (Ligand Donor)	false
N10	OD2	ASP- 228	2.65	0	Ionic (Ligand Cationic)	false
N10	OD1	ASP- 228	3.86	0	Ionic (Ligand Cationic)	false
N7	O	GLY- 230	2.83	166.42	H-Bond (Ligand Donor)	false
C3	CB	THR- 329	4.18	0	Hydrophobic	false
C3	CG2	VAL- 332	3.89	0	Hydrophobic	false