scPDB - 4k8s entry

Protein Data Bank Entry:

PDB ID : 4k8s

Resolution :2.390 Å

Experimental Method : X-ray

Deposition Date : 2013-04-18

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
C	100 %

Ligand binding site composition:

B-Factor:	42.163
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.854	857.250

% Hydrophobic	% Polar
36.61	63.39
According to VolSite

Ligand :

HET Code:	1QT
Formula:	C32H45N2O3
Molecular weight:	505.711 g/mol
DrugBank ID:	-
Buried Surface Area:	66.13 %
Polar Surface area:	75.17 Å2

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

Mass center Coordinates

X	Y	Z
9.47941	-8.55632	49.2471

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
C13	CD1	LEU- 30	4.5	0	Hydrophobic	false
C19	CD2	LEU- 30	3.64	0	Hydrophobic	false
O2	OD1	ASP- 32	3.47	134.18	H-Bond (Ligand Donor)	false
O2	OD2	ASP- 32	2.58	169.5	H-Bond (Ligand Donor)	false
N2	O	GLY- 34	3.09	142.76	H-Bond (Ligand Donor)	false
C32	CB	SER- 35	4.06	0	Hydrophobic	false
C31	CG1	VAL- 69	4.01	0	Hydrophobic	false
C31	CD2	TYR- 71	3.86	0	Hydrophobic	false
C21	CD2	TYR- 71	4.24	0	Hydrophobic	false
C20	CD2	TYR- 71	3.97	0	Hydrophobic	false
C17	CB	TYR- 71	4.39	0	Hydrophobic	false
O1	N	THR- 72	3.33	133.2	H-Bond (Protein Donor)	false
C7	CG2	THR- 72	3.77	0	Hydrophobic	false
C8	CG	GLN- 73	3.96	0	Hydrophobic	false
C11	CD1	ILE- 110	4.28	0	Hydrophobic	false
C13	CZ2	TRP- 115	4.18	0	Hydrophobic	false
C20	CD1	ILE- 118	4.05	0	Hydrophobic	false
C2	CZ	TYR- 198	3.87	0	Hydrophobic	false
C24	CD1	ILE- 226	4.28	0	Hydrophobic	false
C2	CD1	ILE- 226	3.98	0	Hydrophobic	false
N2	OD1	ASP- 228	3.69	0	Ionic (Ligand Cationic)	false
N2	OD2	ASP- 228	2.79	0	Ionic (Ligand Cationic)	false
N2	OD2	ASP- 228	2.79	144.18	H-Bond (Ligand Donor)	false
N1	O	GLY- 230	2.63	171.66	H-Bond (Ligand Donor)	false
C3	CB	THR- 329	4.22	0	Hydrophobic	false
C3	CG2	VAL- 332	3.92	0	Hydrophobic	false