scPDB - 4k9h entry

Protein Data Bank Entry:

PDB ID : 4k9h

Resolution :2.290 Å

Experimental Method : X-ray

Deposition Date : 2013-04-19

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:	37.507
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.665	779.625

% Hydrophobic	% Polar
30.30	69.70
According to VolSite

Ligand :

HET Code:	1QU
Formula:	C33H38F3N4O4
Molecular weight:	611.674 g/mol
DrugBank ID:	-
Buried Surface Area:	66.04 %
Polar Surface area:	106.55 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
9.80377	-7.76589	49.4798

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
C24	CD1	LEU- 30	3.79	0	Hydrophobic	false
O3	OD2	ASP- 32	2.81	164.96	H-Bond (Ligand Donor)	false
N4	O	GLY- 34	3.03	124.63	H-Bond (Ligand Donor)	false
F1	CB	SER- 35	3.4	0	Hydrophobic	false
F2	CG1	VAL- 69	4.12	0	Hydrophobic	false
F1	CG1	VAL- 69	3.72	0	Hydrophobic	false
C31	CD1	TYR- 71	3.65	0	Hydrophobic	false
C21	CB	TYR- 71	4.02	0	Hydrophobic	false
C28	CD1	TYR- 71	4.04	0	Hydrophobic	false
F1	CE1	TYR- 71	3.44	0	Hydrophobic	false
O2	N	GLN- 73	3.2	147.32	H-Bond (Protein Donor)	false
C9	CD1	ILE- 110	3.69	0	Hydrophobic	false
C25	CD1	ILE- 118	3.93	0	Hydrophobic	false
F3	CD1	ILE- 126	3.98	0	Hydrophobic	false
N4	OD1	ASP- 228	3.96	0	Ionic (Ligand Cationic)	false
N4	OD2	ASP- 228	2.87	0	Ionic (Ligand Cationic)	false
N4	OD2	ASP- 228	2.87	136.34	H-Bond (Ligand Donor)	false
N3	O	GLY- 230	3.05	167.43	H-Bond (Ligand Donor)	false
C7	CB	THR- 232	4.14	0	Hydrophobic	false
C3	CB	ASN- 233	3.53	0	Hydrophobic	false
C2	CD	ARG- 235	3.69	0	Hydrophobic	false