scPDB - 4ewo entry

Protein Data Bank Entry:

PDB ID : 4ewo

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2012-04-27

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:	17.877
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.894	850.500

% Hydrophobic	% Polar
28.57	71.43
According to VolSite

Ligand :

HET Code:	996
Formula:	C26H41N4O2
Molecular weight:	441.629 g/mol
DrugBank ID:	-
Buried Surface Area:	60.13 %
Polar Surface area:	83.76 Å2

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

Mass center Coordinates

X	Y	Z
5.82259	4.92169	-19.051

Binding mode :

What is Poseview ?

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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
C26	CD2	LEU- 78	3.68	0	Hydrophobic	false
C22	CD2	LEU- 78	4.18	0	Hydrophobic	false
O1	OD1	ASP- 80	3.44	140.19	H-Bond (Ligand Donor)	false
O1	OD2	ASP- 80	2.5	160.52	H-Bond (Ligand Donor)	false
N11	O	GLY- 82	3.11	149.25	H-Bond (Ligand Donor)	false
C30	CB	SER- 83	4.37	0	Hydrophobic	false
C28	CG1	VAL- 117	4.45	0	Hydrophobic	false
C32	CG1	VAL- 117	3.95	0	Hydrophobic	false
C13	CD1	TYR- 119	3.95	0	Hydrophobic	false
C23	CB	TYR- 119	3.99	0	Hydrophobic	false
C9	CD1	TYR- 119	4.02	0	Hydrophobic	false
C28	CD1	TYR- 119	3.98	0	Hydrophobic	false
O21	N	THR- 120	3.04	144.87	H-Bond (Protein Donor)	false
C5	CB	THR- 120	4.19	0	Hydrophobic	false
C13	CD1	ILE- 166	3.75	0	Hydrophobic	false
C30	CD1	ILE- 174	3.96	0	Hydrophobic	false
C32	CG	ARG- 176	4.04	0	Hydrophobic	false
C3	CE1	TYR- 246	3.77	0	Hydrophobic	false
C30	CE1	TYR- 246	4.14	0	Hydrophobic	false
C3	CD1	ILE- 274	4.05	0	Hydrophobic	false
C15	CD1	ILE- 274	4.33	0	Hydrophobic	false
N11	OD1	ASP- 276	3.77	0	Ionic (Ligand Cationic)	false
N11	OD2	ASP- 276	2.58	0	Ionic (Ligand Cationic)	false
N11	OD2	ASP- 276	2.58	175.47	H-Bond (Ligand Donor)	false
N7	O	GLY- 278	2.77	162.52	H-Bond (Ligand Donor)	false
C5	CB	THR- 279	4.5	0	Hydrophobic	false
C4	CB	THR- 377	3.91	0	Hydrophobic	false
C4	CG2	VAL- 380	4.02	0	Hydrophobic	false
O21	O	HOH- 652	2.79	137.2	H-Bond (Protein Donor)	false