scPDB - 3qi1 entry

Protein Data Bank Entry:

PDB ID : 3qi1

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2011-01-26

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:	21.840
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.402	516.375

% Hydrophobic	% Polar
35.95	64.05
According to VolSite

Ligand :

HET Code:	C6A
Formula:	C29H39F2N2O3
Molecular weight:	501.628 g/mol
DrugBank ID:	-
Buried Surface Area:	62.77 %
Polar Surface area:	75.17 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
1.56733	16.4092	-10.3475

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
F8	CD1	LEU- 36	3.83	0	Hydrophobic	false
O32	OD1	ASP- 38	2.5	143.66	H-Bond (Ligand Donor)	false
O32	OD2	ASP- 38	3.14	149.24	H-Bond (Ligand Donor)	false
N13	O	GLY- 40	2.95	148.11	H-Bond (Ligand Donor)	false
C24	CB	SER- 41	4.5	0	Hydrophobic	false
C28	CB	SER- 41	4.21	0	Hydrophobic	false
C26	CG1	VAL- 75	3.67	0	Hydrophobic	false
F7	CD2	TYR- 77	3.84	0	Hydrophobic	false
C9	CD1	TYR- 77	3.94	0	Hydrophobic	false
C11	CD1	TYR- 77	4.19	0	Hydrophobic	false
C24	CD1	TYR- 77	3.64	0	Hydrophobic	false
C1	CG	TYR- 77	3.45	0	Hydrophobic	false
C35	CB	THR- 78	4.21	0	Hydrophobic	false
O36	N	THR- 78	3.2	159.81	H-Bond (Protein Donor)	false
F7	CD1	PHE- 114	3.22	0	Hydrophobic	false
F8	CD1	ILE- 116	4.04	0	Hydrophobic	false
F8	CZ2	TRP- 121	3.44	0	Hydrophobic	false
C9	CD1	ILE- 124	3.78	0	Hydrophobic	false
C2	CD1	ILE- 124	3.99	0	Hydrophobic	false
C28	CD1	ILE- 132	4.2	0	Hydrophobic	false
C26	CG	ARG- 134	4.07	0	Hydrophobic	false
C28	CE1	TYR- 204	4.21	0	Hydrophobic	false
C29	CZ	TYR- 204	3.86	0	Hydrophobic	false
C31	CD	LYS- 230	4.21	0	Hydrophobic	false
C19	CD1	ILE- 232	3.96	0	Hydrophobic	false
C29	CD1	ILE- 232	3.81	0	Hydrophobic	false
N13	OD1	ASP- 234	3.95	0	Ionic (Ligand Cationic)	false
N13	OD2	ASP- 234	2.82	0	Ionic (Ligand Cationic)	false
N13	OD2	ASP- 234	2.82	166.63	H-Bond (Ligand Donor)	false
N33	O	GLY- 236	2.89	162.15	H-Bond (Ligand Donor)	false
C30	CB	THR- 335	4.18	0	Hydrophobic	false
C18	CG2	VAL- 338	4.47	0	Hydrophobic	false
C31	CG2	VAL- 338	4.1	0	Hydrophobic	false