scPDB - 3k5f entry

Protein Data Bank Entry:

PDB ID : 3k5f

Resolution :2.250 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
A	100 %

Ligand binding site composition:

B-Factor:	35.949
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.741	897.750

% Hydrophobic	% Polar
28.95	71.05
According to VolSite

Ligand :

HET Code:	AYH
Formula:	C29H47N3O4
Molecular weight:	501.701 g/mol
DrugBank ID:	-
Buried Surface Area:	67.32 %
Polar Surface area:	107.52 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
4.85156	12.1915	27.1676

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
C45	CD1	LEU- 30	4.03	0	Hydrophobic	false
C47	CD2	LEU- 30	4.22	0	Hydrophobic	false
C72	CD1	LEU- 30	4.34	0	Hydrophobic	false
N20	O	GLY- 34	2.89	162.13	H-Bond (Ligand Donor)	false
C25	CB	SER- 35	4.09	0	Hydrophobic	false
C31	CG1	VAL- 69	4.12	0	Hydrophobic	false
C5	CD1	TYR- 71	3.94	0	Hydrophobic	false
C35	CD1	TYR- 71	3.96	0	Hydrophobic	false
C39	CB	TYR- 71	4.06	0	Hydrophobic	false
C9	CB	THR- 72	4.39	0	Hydrophobic	false
C64	CB	THR- 72	3.83	0	Hydrophobic	false
O19	N	THR- 72	3.03	140.12	H-Bond (Protein Donor)	false
O50	N	GLN- 73	3.08	142.39	H-Bond (Protein Donor)	false
C64	CB	GLN- 73	3.75	0	Hydrophobic	false
C35	CD1	ILE- 118	3.88	0	Hydrophobic	false
C25	CD1	ILE- 126	4.19	0	Hydrophobic	false
C28	CB	ILE- 126	4.37	0	Hydrophobic	false
C31	CG	ARG- 128	4.24	0	Hydrophobic	false
C14	CE1	TYR- 198	4.24	0	Hydrophobic	false
C25	CE1	TYR- 198	4.16	0	Hydrophobic	false
C14	CD1	ILE- 226	3.91	0	Hydrophobic	false
O7	OD2	ASP- 228	2.64	167.4	H-Bond (Ligand Donor)	false
N1	O	GLY- 230	3.04	170.63	H-Bond (Ligand Donor)	false
C51	CB	THR- 231	4.34	0	Hydrophobic	false
C61	CG2	THR- 231	4.38	0	Hydrophobic	false
O71	OG1	THR- 232	2.66	153.88	H-Bond (Protein Donor)	false
O71	N	THR- 232	2.94	133.25	H-Bond (Protein Donor)	false