scPDB - 4dpi entry

Protein Data Bank Entry:

PDB ID : 4dpi

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-02-13

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:	14.528
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.425	587.250

% Hydrophobic	% Polar
35.06	64.94
According to VolSite

Ligand :

HET Code:	0N1
Formula:	C34H42N3O4
Molecular weight:	556.715 g/mol
DrugBank ID:	-
Buried Surface Area:	66.62 %
Polar Surface area:	104.27 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-5.1082	1.54088	18.1749

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
C18	CD1	LEU- 78	4.35	0	Hydrophobic	false
C21	CD2	LEU- 78	3.66	0	Hydrophobic	false
O28	OD2	ASP- 80	2.56	164.35	H-Bond (Ligand Donor)	false
N30	O	GLY- 82	3.1	150.98	H-Bond (Ligand Donor)	false
C38	CB	SER- 83	4.18	0	Hydrophobic	false
C40	CG1	VAL- 117	3.5	0	Hydrophobic	false
C41	CD1	TYR- 119	4.15	0	Hydrophobic	false
C27	CD1	TYR- 119	4.02	0	Hydrophobic	false
C40	CD1	TYR- 119	3.92	0	Hydrophobic	false
C2	CB	THR- 120	4.1	0	Hydrophobic	false
C33	CB	THR- 120	4.44	0	Hydrophobic	false
C7	CG2	THR- 120	4.44	0	Hydrophobic	false
O26	N	GLN- 121	3.2	162.18	H-Bond (Protein Donor)	false
C7	CB	GLN- 121	4.09	0	Hydrophobic	false
C2	CB	GLN- 121	3.54	0	Hydrophobic	false
C21	CE1	PHE- 156	4.2	0	Hydrophobic	false
C18	CD1	ILE- 158	3.89	0	Hydrophobic	false
C18	CZ2	TRP- 163	4.07	0	Hydrophobic	false
C41	CD1	ILE- 166	3.96	0	Hydrophobic	false
C21	CD1	ILE- 166	3.9	0	Hydrophobic	false
C39	CB	ILE- 174	3.98	0	Hydrophobic	false
C39	CE1	TYR- 246	4.3	0	Hydrophobic	false
N30	OD2	ASP- 276	2.69	165.31	H-Bond (Ligand Donor)	false
N30	OD2	ASP- 276	2.69	0	Ionic (Ligand Cationic)	false
N24	O	GLY- 278	2.86	159	H-Bond (Ligand Donor)	false
N10	O	GLY- 278	3.29	169.12	H-Bond (Ligand Donor)	false
C2	CG2	THR- 279	4.44	0	Hydrophobic	false
C3	CB	THR- 279	4.41	0	Hydrophobic	false
C16	CB	THR- 280	4.42	0	Hydrophobic	false
C15	CB	ALA- 383	3.56	0	Hydrophobic	false