scPDB - 2ph8 entry

Protein Data Bank Entry:

PDB ID : 2ph8

Resolution :1.700 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:	23.441
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.694	742.500

% Hydrophobic	% Polar
32.27	67.73
According to VolSite

Ligand :

HET Code:	35A
Formula:	C24H34N3O4S
Molecular weight:	460.609 g/mol
DrugBank ID:	DB07019
Buried Surface Area:	70.66 %
Polar Surface area:	112.58 Å2

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

Mass center Coordinates

X	Y	Z
30.0282	42.4072	1.37891

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
C14	CD2	LEU- 30	3.54	0	Hydrophobic	false
N28	OD1	ASP- 32	3.63	0	Ionic (Ligand Cationic)	false
N28	OD2	ASP- 32	2.63	0	Ionic (Ligand Cationic)	false
N28	OD2	ASP- 32	2.63	156.3	H-Bond (Ligand Donor)	false
C27	CB	SER- 35	4.01	0	Hydrophobic	false
C3	CB	TYR- 71	3.96	0	Hydrophobic	false
C6	CD1	TYR- 71	3.89	0	Hydrophobic	false
C27	CD1	TYR- 71	3.97	0	Hydrophobic	false
C4	CB	THR- 72	3.59	0	Hydrophobic	false
C17	CG2	THR- 72	4.11	0	Hydrophobic	false
O26	N	THR- 72	3.14	124.01	H-Bond (Protein Donor)	false
C2	CB	GLN- 73	3.84	0	Hydrophobic	false
C	CB	GLN- 73	3.8	0	Hydrophobic	false
C13	CD1	ILE- 110	3.79	0	Hydrophobic	false
C14	CZ2	TRP- 115	3.83	0	Hydrophobic	false
C6	CD1	ILE- 118	4.17	0	Hydrophobic	false
N28	OD1	ASP- 228	3.36	0	Ionic (Ligand Cationic)	false
N28	OD2	ASP- 228	2.97	0	Ionic (Ligand Cationic)	false
N28	OD2	ASP- 228	2.97	165.92	H-Bond (Ligand Donor)	false
N28	O	GLY- 230	2.88	149.89	H-Bond (Ligand Donor)	false
C17	CG2	THR- 231	4.26	0	Hydrophobic	false
C20	CB	THR- 232	4.43	0	Hydrophobic	false
O22	N	ASN- 233	2.85	156.27	H-Bond (Protein Donor)	false