scPDB - 4i0i entry

Protein Data Bank Entry:

PDB ID : 4i0i

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-11-16

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:	45.251
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.184	1427.625

% Hydrophobic	% Polar
36.88	63.12
According to VolSite

Ligand :

HET Code:	957
Formula:	C24H33F2N2O2S
Molecular weight:	451.593 g/mol
DrugBank ID:	-
Buried Surface Area:	61.46 %
Polar Surface area:	94.18 Å2

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

Mass center Coordinates

X	Y	Z
17.7852	-16.2955	-1.08977

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
F27	CD1	LEU- 36	3.73	0	Hydrophobic	false
O29	OD1	ASP- 38	2.57	163.78	H-Bond (Ligand Donor)	false
O29	OD2	ASP- 38	3.41	138.7	H-Bond (Ligand Donor)	false
N7	O	GLY- 40	2.94	150.14	H-Bond (Ligand Donor)	false
C17	CB	SER- 41	4.39	0	Hydrophobic	false
C18	CG1	VAL- 75	3.77	0	Hydrophobic	false
C5	CD1	TYR- 77	3.92	0	Hydrophobic	false
C14	CD1	TYR- 77	4.01	0	Hydrophobic	false
C20	CD1	TYR- 77	4.01	0	Hydrophobic	false
C26	CB	TYR- 77	4.01	0	Hydrophobic	false
F28	CD2	TYR- 77	4.02	0	Hydrophobic	false
C1	CB	THR- 78	4.2	0	Hydrophobic	false
O19	N	THR- 78	3.21	139.04	H-Bond (Protein Donor)	false
F28	CD1	PHE- 114	3.25	0	Hydrophobic	false
F27	CD1	ILE- 116	3.54	0	Hydrophobic	false
F27	CH2	TRP- 121	3.82	0	Hydrophobic	false
C20	CD1	ILE- 124	3.79	0	Hydrophobic	false
C17	CD1	ILE- 132	3.98	0	Hydrophobic	false
C18	CG	ARG- 134	3.98	0	Hydrophobic	false
C17	CE1	TYR- 204	4.31	0	Hydrophobic	false
C31	CE1	TYR- 204	3.42	0	Hydrophobic	false
C31	CD1	ILE- 232	3.54	0	Hydrophobic	false
N7	OD1	ASP- 234	3.8	0	Ionic (Ligand Cationic)	false
N7	OD2	ASP- 234	2.66	0	Ionic (Ligand Cationic)	false
N7	OD2	ASP- 234	2.66	161.76	H-Bond (Ligand Donor)	false
N3	O	GLY- 236	2.92	166.83	H-Bond (Ligand Donor)	false
O19	O	HOH- 711	2.79	135.4	H-Bond (Protein Donor)	false