scPDB - 3kmy entry

Protein Data Bank Entry:

PDB ID : 3kmy

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-11-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	4.500	4.500	4.500	0.000	4.500	1

List of CHEMBLId :

CHEMBL575232

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:	18.831
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.777	924.750

% Hydrophobic	% Polar
37.59	62.41
According to VolSite

Ligand :

HET Code:	D8Y
Formula:	C13H13ClN2
Molecular weight:	232.709 g/mol
DrugBank ID:	-
Buried Surface Area:	58.15 %
Polar Surface area:	38.9 Å2

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

Mass center Coordinates

X	Y	Z
22.0464	11.851	22.0278

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
N2	OD2	ASP- 93	2.81	146.57	H-Bond (Ligand Donor)	false
C6	CB	SER- 96	4.38	0	Hydrophobic	false
CL1	CD2	TYR- 132	3.43	0	Hydrophobic	false
C6	CZ	TYR- 132	3.83	0	Hydrophobic	false
C10	CG	GLN- 134	4.07	0	Hydrophobic	false
CL1	CD1	PHE- 169	3.4	0	Hydrophobic	false
C7	CD1	ILE- 179	3.84	0	Hydrophobic	false
N1	OD2	ASP- 289	2.63	177.67	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 289	3.14	177.21	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 289	3.47	126.27	H-Bond (Ligand Donor)	false