scPDB - 4d89 entry

Protein Data Bank Entry:

PDB ID : 4d89

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2012-01-10

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:	18.306
Number of residues:	48
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.793	793.125

% Hydrophobic	% Polar
30.64	69.36
According to VolSite

Ligand :

HET Code:	BXD
Formula:	C28H38F4N2O5S
Molecular weight:	590.670 g/mol
DrugBank ID:	-
Buried Surface Area:	64.8 %
Polar Surface area:	119.26 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
29.8232	72.2368	18.3685

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
F1	CB	GLN- 60	4.31	0	Hydrophobic	false
C2	CD1	LEU- 78	4.42	0	Hydrophobic	false
F3	CD2	LEU- 78	3.29	0	Hydrophobic	false
C14	CD2	LEU- 78	3.89	0	Hydrophobic	false
O62	OD2	ASP- 80	2.67	160.48	H-Bond (Ligand Donor)	false
N34	O	GLY- 82	2.94	142.55	H-Bond (Ligand Donor)	false
C58	CB	SER- 83	3.72	0	Hydrophobic	false
C54	CG1	VAL- 117	4.29	0	Hydrophobic	false
C58	CG1	VAL- 117	3.66	0	Hydrophobic	false
C11	CB	TYR- 119	4.2	0	Hydrophobic	false
C21	CD1	TYR- 119	4.13	0	Hydrophobic	false
C58	CE1	TYR- 119	3.68	0	Hydrophobic	false
F64	CD2	TYR- 119	4.01	0	Hydrophobic	false
C19	CD1	TYR- 119	3.79	0	Hydrophobic	false
O33	N	THR- 120	2.97	130.41	H-Bond (Protein Donor)	false
C75	CG	GLN- 121	3.48	0	Hydrophobic	false
F64	CE1	PHE- 156	3.64	0	Hydrophobic	false
C72	CD1	ILE- 158	4.4	0	Hydrophobic	false
F1	CZ2	TRP- 163	3.71	0	Hydrophobic	false
C16	CD1	ILE- 166	4.05	0	Hydrophobic	false
C50	CB	ILE- 174	3.92	0	Hydrophobic	false
C50	CE1	TYR- 246	4.25	0	Hydrophobic	false
N34	OD2	ASP- 276	2.68	169	H-Bond (Ligand Donor)	false
N34	OD2	ASP- 276	2.68	0	Ionic (Ligand Cationic)	false
C25	CB	THR- 279	4.49	0	Hydrophobic	false
C29	CB	THR- 279	4.48	0	Hydrophobic	false