scPDB - 2ph6 entry

Protein Data Bank Entry:

PDB ID : 2ph6

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-04-10

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:	26.613
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.671	820.125

% Hydrophobic	% Polar
31.28	68.72
According to VolSite

Ligand :

HET Code:	712
Formula:	C28H33FN3O5S
Molecular weight:	542.642 g/mol
DrugBank ID:	-
Buried Surface Area:	73.94 %
Polar Surface area:	128.8 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
30.2599	42.5257	2.34792

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
F	CE1	TYR- 14	3.37	0	Hydrophobic	false
C32	CD2	LEU- 30	3.97	0	Hydrophobic	false
C9	CD2	LEU- 30	3.49	0	Hydrophobic	false
N	OD2	ASP- 32	3.64	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 32	2.59	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 32	2.59	161.41	H-Bond (Ligand Donor)	false
C3	CB	SER- 35	4.07	0	Hydrophobic	false
C3	CD1	TYR- 71	4.19	0	Hydrophobic	false
C4	CG	TYR- 71	3.66	0	Hydrophobic	false
C10	CB	TYR- 71	3.97	0	Hydrophobic	false
O2	N	THR- 72	3.37	127.72	H-Bond (Protein Donor)	false
C15	CG2	THR- 72	4.38	0	Hydrophobic	false
C33	CB	THR- 72	3.83	0	Hydrophobic	false
C8	CG	GLN- 73	4.25	0	Hydrophobic	false
C33	CB	GLN- 73	3.91	0	Hydrophobic	false
C14	CB	GLN- 73	3.85	0	Hydrophobic	false
C32	CD1	ILE- 110	4.03	0	Hydrophobic	false
C32	CZ2	TRP- 115	3.88	0	Hydrophobic	false
C6	CD1	ILE- 118	3.98	0	Hydrophobic	false
N	OD1	ASP- 228	3.27	120.32	H-Bond (Ligand Donor)	false
N	OD2	ASP- 228	2.84	173.38	H-Bond (Ligand Donor)	false
N	OD1	ASP- 228	3.27	0	Ionic (Ligand Cationic)	false
N	OD2	ASP- 228	2.84	0	Ionic (Ligand Cationic)	false
N	O	GLY- 230	3.33	143.38	H-Bond (Ligand Donor)	false
N19	O	GLY- 230	2.82	164.28	H-Bond (Ligand Donor)	false
C14	CB	THR- 231	4.39	0	Hydrophobic	false
C15	CG2	THR- 231	4.2	0	Hydrophobic	false
C11	CB	THR- 232	4.32	0	Hydrophobic	false
C29	CG2	THR- 232	4.02	0	Hydrophobic	false
O22	N	ASN- 233	2.78	159.61	H-Bond (Protein Donor)	false
C24	CD	ARG- 235	4.29	0	Hydrophobic	false
C28	CB	ALA- 335	3.82	0	Hydrophobic	false