scPDB - 3ixk entry

Protein Data Bank Entry:

PDB ID : 3ixk

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2009-09-04

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	2 %
B	98 %

Ligand binding site composition:

B-Factor:	32.118
Number of residues:	54
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.585	664.875

% Hydrophobic	% Polar
34.01	65.99
According to VolSite

Ligand :

HET Code:	929
Formula:	C44H53F2N5O8S
Molecular weight:	849.982 g/mol
DrugBank ID:	-
Buried Surface Area:	65.25 %
Polar Surface area:	191.61 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-19.1064	22.1395	0.8708

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
C37	CD2	LEU- 78	3.94	0	Hydrophobic	false
C26	CD2	LEU- 78	4.03	0	Hydrophobic	false
C6	CB	ASP- 80	4.24	0	Hydrophobic	false
O1	OD1	ASP- 80	2.7	153.99	H-Bond (Ligand Donor)	false
N2	O	GLY- 82	2.98	157.44	H-Bond (Ligand Donor)	false
C11	CB	SER- 83	3.98	0	Hydrophobic	false
C12	CG1	VAL- 117	3.56	0	Hydrophobic	false
N3	O	PRO- 118	2.85	147.65	H-Bond (Ligand Donor)	false
C19	CB	PRO- 118	3.77	0	Hydrophobic	false
C6	CD1	TYR- 119	3.74	0	Hydrophobic	false
C20	CG	TYR- 119	3.75	0	Hydrophobic	false
C22	CB	TYR- 119	4.2	0	Hydrophobic	false
C12	CE1	TYR- 119	4.49	0	Hydrophobic	false
C1	CD1	TYR- 119	3.97	0	Hydrophobic	false
C43	CG2	THR- 120	3.86	0	Hydrophobic	false
C33	CB	THR- 120	4.13	0	Hydrophobic	false
O3	N	THR- 120	3.27	141.01	H-Bond (Protein Donor)	false
C24	CG	GLN- 121	4.29	0	Hydrophobic	false
F2	CG	GLN- 121	3.35	0	Hydrophobic	false
C33	CB	GLN- 121	3.96	0	Hydrophobic	false
C27	CB	GLN- 121	3.84	0	Hydrophobic	false
C23	CB	GLN- 121	3.58	0	Hydrophobic	false
C20	CE1	PHE- 156	4.28	0	Hydrophobic	false
F1	CD1	ILE- 158	3.41	0	Hydrophobic	false
F1	CZ2	TRP- 163	3.3	0	Hydrophobic	false
C6	CD1	ILE- 166	3.88	0	Hydrophobic	false
C20	CD1	ILE- 166	4.27	0	Hydrophobic	false
C11	CD1	ILE- 174	3.6	0	Hydrophobic	false
C12	CG	ARG- 176	4.5	0	Hydrophobic	false
C7	CE1	TYR- 246	4.3	0	Hydrophobic	false
C11	CE1	TYR- 246	4.19	0	Hydrophobic	false
O4	OH	TYR- 246	2.75	164.68	H-Bond (Protein Donor)	false
C7	CD1	ILE- 274	4.12	0	Hydrophobic	false
N4	O	GLY- 278	2.98	174.53	H-Bond (Ligand Donor)	false
N1	O	GLY- 278	3.04	174.19	H-Bond (Ligand Donor)	false
C27	CB	THR- 279	4.34	0	Hydrophobic	false
C32	CG2	THR- 279	3.87	0	Hydrophobic	false
O1	OG1	THR- 279	3.49	128.7	H-Bond (Protein Donor)	false
C39	CG2	THR- 280	4.27	0	Hydrophobic	false
C38	CB	THR- 280	4.23	0	Hydrophobic	false
C31	CB	THR- 280	4.39	0	Hydrophobic	false
O7	N	ASN- 281	3.02	149.66	H-Bond (Protein Donor)	false
C43	CD	ARG- 283	3.7	0	Hydrophobic	false
O8	OG	SER- 373	3.4	126.98	H-Bond (Protein Donor)	false
C16	CG2	THR- 377	4.25	0	Hydrophobic	false
C40	CB	ALA- 383	3.79	0	Hydrophobic	false