scPDB - 3k5c entry

Protein Data Bank Entry:

PDB ID : 3k5c

Resolution :2.120 Å

Experimental Method : X-ray

Deposition Date : 2009-10-07

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:	39.107
Number of residues:	45
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.930	924.750

% Hydrophobic	% Polar
29.20	70.80
According to VolSite

Ligand :

HET Code:	0BI
Formula:	C35H46N3O4
Molecular weight:	572.757 g/mol
DrugBank ID:	-
Buried Surface Area:	61.39 %
Polar Surface area:	96.43 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
9.24964	-41.3748	48.9886

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
C19	CD1	LEU- 30	4.19	0	Hydrophobic	false
C9	CD2	LEU- 30	3.49	0	Hydrophobic	false
O54	OD1	ASP- 32	3.25	137.33	H-Bond (Ligand Donor)	false
O54	OD2	ASP- 32	2.58	161.2	H-Bond (Ligand Donor)	false
N59	O	GLY- 34	3.09	151.82	H-Bond (Ligand Donor)	false
C80	CB	SER- 35	3.88	0	Hydrophobic	false
C84	CB	SER- 35	4.35	0	Hydrophobic	false
C80	CG1	VAL- 69	3.48	0	Hydrophobic	false
C5	CD1	TYR- 71	4.04	0	Hydrophobic	false
C16	CB	TYR- 71	4.42	0	Hydrophobic	false
C52	CD1	TYR- 71	4.14	0	Hydrophobic	false
C80	CD1	TYR- 71	3.81	0	Hydrophobic	false
C42	CG2	THR- 72	4.11	0	Hydrophobic	false
C37	CB	THR- 72	3.64	0	Hydrophobic	false
O51	N	THR- 72	3.33	146.56	H-Bond (Protein Donor)	false
O51	OG1	THR- 72	3.46	123.15	H-Bond (Protein Donor)	false
C25	CD1	ILE- 110	4.35	0	Hydrophobic	false
C12	CD1	ILE- 110	4.32	0	Hydrophobic	false
C22	CD1	ILE- 110	3.88	0	Hydrophobic	false
C19	CZ2	TRP- 115	4.33	0	Hydrophobic	false
C5	CD1	ILE- 118	3.86	0	Hydrophobic	false
C84	CD1	ILE- 126	3.63	0	Hydrophobic	false
C62	CE1	TYR- 198	3.52	0	Hydrophobic	false
C84	CE1	TYR- 198	3.95	0	Hydrophobic	false
C62	CD1	ILE- 226	3.33	0	Hydrophobic	false
N59	OD1	ASP- 228	3.88	0	Ionic (Ligand Cationic)	false
N59	OD2	ASP- 228	2.63	0	Ionic (Ligand Cationic)	false
N59	OD2	ASP- 228	2.63	160.58	H-Bond (Ligand Donor)	false
N1	O	GLY- 230	3.04	167.25	H-Bond (Ligand Donor)	false
C34	CB	THR- 231	4.3	0	Hydrophobic	false
C33	CG2	THR- 231	4.33	0	Hydrophobic	false
C28	CB	THR- 232	3.93	0	Hydrophobic	false
C46	CD	ARG- 235	3.89	0	Hydrophobic	false
C65	CG2	VAL- 332	4.5	0	Hydrophobic	false
O51	O	HOH- 437	2.75	153.35	H-Bond (Protein Donor)	false