scPDB - 4dh6 entry

Protein Data Bank Entry:

PDB ID : 4dh6

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2012-01-27

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:	33.870
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.013	830.250

% Hydrophobic	% Polar
36.59	63.41
According to VolSite

Ligand :

HET Code:	0KN
Formula:	C31H44N3O6
Molecular weight:	554.698 g/mol
DrugBank ID:	-
Buried Surface Area:	64.12 %
Polar Surface area:	115.75 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
67.2745	48.4877	9.05417

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
C10	CD2	LEU- 30	3.62	0	Hydrophobic	false
O14	OD1	ASP- 32	3.24	135.99	H-Bond (Ligand Donor)	false
N5	O	GLY- 34	2.82	143.15	H-Bond (Ligand Donor)	false
C24	CB	SER- 35	4.29	0	Hydrophobic	false
C26	CB	SER- 35	4.08	0	Hydrophobic	false
C20	CB	SER- 35	4.45	0	Hydrophobic	false
C24	CG1	VAL- 69	4.47	0	Hydrophobic	false
C27	CG1	VAL- 69	3.71	0	Hydrophobic	false
C24	CD1	TYR- 71	3.76	0	Hydrophobic	false
C3	CD1	TYR- 71	4.05	0	Hydrophobic	false
C7	CD1	TYR- 71	4.19	0	Hydrophobic	false
C13	CB	TYR- 71	3.89	0	Hydrophobic	false
O36	OG1	THR- 72	3.17	160.97	H-Bond (Protein Donor)	false
C40	CG2	THR- 72	3.73	0	Hydrophobic	false
C18	CG2	THR- 72	4.05	0	Hydrophobic	false
C33	CD1	ILE- 110	3.52	0	Hydrophobic	false
C33	CZ2	TRP- 115	3.66	0	Hydrophobic	false
C7	CD1	ILE- 118	3.78	0	Hydrophobic	false
C26	CD1	ILE- 126	4	0	Hydrophobic	false
C27	CD	ARG- 128	3.98	0	Hydrophobic	false
C31	CZ	TYR- 198	3.91	0	Hydrophobic	false
C26	CE1	TYR- 198	4.48	0	Hydrophobic	false
C19	CD1	ILE- 226	4.16	0	Hydrophobic	false
C31	CD1	ILE- 226	4.05	0	Hydrophobic	false
N5	OD2	ASP- 228	2.74	167.26	H-Bond (Ligand Donor)	false
N5	OD2	ASP- 228	2.74	0	Ionic (Ligand Cationic)	false
N1	O	GLY- 230	2.69	176.29	H-Bond (Ligand Donor)	false
C40	CG2	THR- 231	3.94	0	Hydrophobic	false
C30	CB	THR- 329	3.59	0	Hydrophobic	false
C30	CG2	VAL- 332	3.71	0	Hydrophobic	false