scPDB - 4lxa entry

Protein Data Bank Entry:

PDB ID : 4lxa

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2013-07-29

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
C	100 %

Ligand binding site composition:

B-Factor:	35.380
Number of residues:	48
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.930	850.500

% Hydrophobic	% Polar
29.37	70.63
According to VolSite

Ligand :

HET Code:	1YS
Formula:	C26H31F7N2O3S
Molecular weight:	584.590 g/mol
DrugBank ID:	-
Buried Surface Area:	64.92 %
Polar Surface area:	103.79 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
8.90015	-42.7117	48.8044

Binding mode :

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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
F70	CB	GLN- 12	4.31	0	Hydrophobic	false
C14	CD2	LEU- 30	3.69	0	Hydrophobic	false
F69	CD1	LEU- 30	3.26	0	Hydrophobic	false
O61	OD1	ASP- 32	3.46	146.55	H-Bond (Ligand Donor)	false
O61	OD2	ASP- 32	2.6	155.89	H-Bond (Ligand Donor)	false
N33	O	GLY- 34	3.02	148.7	H-Bond (Ligand Donor)	false
C57	CB	SER- 35	3.66	0	Hydrophobic	false
C53	CG1	VAL- 69	4.25	0	Hydrophobic	false
C57	CG1	VAL- 69	3.59	0	Hydrophobic	false
C11	CB	TYR- 71	4.14	0	Hydrophobic	false
C21	CD1	TYR- 71	4.08	0	Hydrophobic	false
C57	CE1	TYR- 71	3.77	0	Hydrophobic	false
F63	CD2	TYR- 71	4.08	0	Hydrophobic	false
C19	CD1	TYR- 71	3.69	0	Hydrophobic	false
C25	CB	THR- 72	4.5	0	Hydrophobic	false
C46	CB	THR- 72	4.49	0	Hydrophobic	false
O32	N	THR- 72	2.86	133.68	H-Bond (Protein Donor)	false
F63	CE1	PHE- 108	3.66	0	Hydrophobic	false
F3	CG1	ILE- 110	3.98	0	Hydrophobic	false
F70	CZ2	TRP- 115	3.9	0	Hydrophobic	false
C16	CD1	ILE- 118	3.88	0	Hydrophobic	false
C49	CB	ILE- 126	3.83	0	Hydrophobic	false
C49	CE1	TYR- 198	4.12	0	Hydrophobic	false
N33	OD2	ASP- 228	2.78	161.52	H-Bond (Ligand Donor)	false
N33	OD2	ASP- 228	2.78	0	Ionic (Ligand Cationic)	false
F4	CB	THR- 232	4.34	0	Hydrophobic	false