scPDB - 2p8h entry

Protein Data Bank Entry:

PDB ID : 2p8h

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2007-03-22

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:	19.101
Number of residues:	55
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	8
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.573	408.375

% Hydrophobic	% Polar
37.19	62.81
According to VolSite

Ligand :

HET Code:	MY9
Formula:	C33H41FN5O6S
Molecular weight:	654.772 g/mol
DrugBank ID:	-
Buried Surface Area:	69.13 %
Polar Surface area:	161.1 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
30.3913	41.3006	2.18759

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
F1	CD1	TYR- 14	3.47	0	Hydrophobic	false
C18	CD2	LEU- 30	3.75	0	Hydrophobic	false
C26	CD2	LEU- 30	3.34	0	Hydrophobic	false
O5	OD2	ASP- 32	2.79	172.77	H-Bond (Ligand Donor)	false
N4	O	GLY- 34	3	163.15	H-Bond (Ligand Donor)	false
C20	CD1	TYR- 71	3.54	0	Hydrophobic	false
C22	CB	TYR- 71	3.72	0	Hydrophobic	false
C27	CD1	TYR- 71	4.06	0	Hydrophobic	false
C12	CB	THR- 72	4.12	0	Hydrophobic	false
C16	CG2	THR- 72	3.85	0	Hydrophobic	false
O4	N	THR- 72	3.19	120.39	H-Bond (Protein Donor)	false
O6	N	THR- 72	2.95	154.27	H-Bond (Protein Donor)	false
O1	NE2	GLN- 73	3.33	139.95	H-Bond (Protein Donor)	false
O4	N	GLN- 73	3.09	150.26	H-Bond (Protein Donor)	false
C11	CB	GLN- 73	3.84	0	Hydrophobic	false
C18	CD1	ILE- 110	4.06	0	Hydrophobic	false
C18	CZ2	TRP- 115	4.1	0	Hydrophobic	false
C26	CD1	ILE- 118	3.87	0	Hydrophobic	false
C33	CE1	TYR- 198	3.2	0	Hydrophobic	false
C32	CD1	ILE- 226	4.13	0	Hydrophobic	false
C33	CD1	ILE- 226	3.68	0	Hydrophobic	false
N4	OD2	ASP- 228	2.69	159.5	H-Bond (Ligand Donor)	false
N4	OD2	ASP- 228	2.69	0	Ionic (Ligand Cationic)	false
N4	OD1	ASP- 228	3.72	0	Ionic (Ligand Cationic)	false
N1	O	GLY- 230	3.28	155.5	H-Bond (Ligand Donor)	false
N3	O	GLY- 230	3.02	155.04	H-Bond (Ligand Donor)	false
C12	CG2	THR- 231	4.15	0	Hydrophobic	false
C4	CG2	THR- 232	4.29	0	Hydrophobic	false
C14	CB	THR- 232	4.3	0	Hydrophobic	false
C3	CB	THR- 232	4.34	0	Hydrophobic	false
O2	N	ASN- 233	3	165.87	H-Bond (Protein Donor)	false
C16	CD	ARG- 235	4.33	0	Hydrophobic	false
C32	CG2	VAL- 332	4.24	0	Hydrophobic	false
C5	CB	ALA- 335	3.73	0	Hydrophobic	false