scPDB - 3rtn entry

Protein Data Bank Entry:

PDB ID : 3rtn

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2011-05-03

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:	40.604
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.989	796.500

% Hydrophobic	% Polar
45.76	54.24
According to VolSite

Ligand :

HET Code:	RTN
Formula:	C25H29N3O
Molecular weight:	387.517 g/mol
DrugBank ID:	-
Buried Surface Area:	60.32 %
Polar Surface area:	68 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
67.5512	48.9056	10.7078

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
N7	OD2	ASP- 32	2.65	170.07	H-Bond (Ligand Donor)	false
N28	OD1	ASP- 32	2.87	167.11	H-Bond (Ligand Donor)	false
N28	OD2	ASP- 32	3.32	130.42	H-Bond (Ligand Donor)	false
N21	O	GLY- 34	2.89	134	H-Bond (Ligand Donor)	false
C24	CB	SER- 35	4.13	0	Hydrophobic	false
C26	CG1	VAL- 69	4.43	0	Hydrophobic	false
C17	CD2	TYR- 71	3.71	0	Hydrophobic	false
C27	CD1	TYR- 71	4.07	0	Hydrophobic	false
C11	CB	TYR- 71	3.79	0	Hydrophobic	false
C12	CB	TYR- 71	3.78	0	Hydrophobic	false
C17	CD1	PHE- 108	4.49	0	Hydrophobic	false
C15	CB	PHE- 108	4.23	0	Hydrophobic	false
C3	CD1	ILE- 118	3.53	0	Hydrophobic	false
C24	CD1	ILE- 126	3.96	0	Hydrophobic	false
C25	CD	ARG- 128	4.3	0	Hydrophobic	false
C23	CZ	TYR- 198	3.78	0	Hydrophobic	false
N28	OD2	ASP- 228	2.98	156.07	H-Bond (Ligand Donor)	false