scPDB - 3qbh entry

Protein Data Bank Entry:

PDB ID : 3qbh

Resolution :2.240 Å

Experimental Method : X-ray

Deposition Date : 2011-01-13

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
B	100 %

Ligand binding site composition:

B-Factor:	40.578
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.105	975.375

% Hydrophobic	% Polar
41.87	58.13
According to VolSite

Ligand :

HET Code:	QBH
Formula:	C29H40N2O6S
Molecular weight:	544.703 g/mol
DrugBank ID:	-
Buried Surface Area:	66.48 %
Polar Surface area:	124.55 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
16.4759	6.66508	-19.5036

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
C18	CD2	LEU- 30	3.52	0	Hydrophobic	false
C18	CD2	LEU- 30	3.52	0	Hydrophobic	false
O50	OD2	ASP- 32	2.56	156.69	H-Bond (Ligand Donor)	false
O50	OD1	ASP- 32	3.35	137.1	H-Bond (Ligand Donor)	false
N52	O	GLY- 34	3.04	142.34	H-Bond (Ligand Donor)	false
C69	CB	SER- 35	3.75	0	Hydrophobic	false
C69	CG1	VAL- 69	3.77	0	Hydrophobic	false
C14	CD1	TYR- 71	4.27	0	Hydrophobic	false
C69	CE1	TYR- 71	3.65	0	Hydrophobic	false
C9	CD1	TYR- 71	3.8	0	Hydrophobic	false
C65	CB	THR- 72	4.28	0	Hydrophobic	false
O78	N	GLN- 73	3.4	153.98	H-Bond (Protein Donor)	false
O26	O	PHE- 108	2.58	145.95	H-Bond (Ligand Donor)	false
C21	CD1	ILE- 110	4.49	0	Hydrophobic	false
C28	CD1	ILE- 110	3.71	0	Hydrophobic	false
C36	CD1	ILE- 110	3.53	0	Hydrophobic	false
C28	CZ2	TRP- 115	3.91	0	Hydrophobic	false
C14	CD1	ILE- 118	3.95	0	Hydrophobic	false
C73	CB	ILE- 126	3.72	0	Hydrophobic	false
C73	CE1	TYR- 198	4.2	0	Hydrophobic	false
N52	OD2	ASP- 228	2.72	165.01	H-Bond (Ligand Donor)	false
N52	OD2	ASP- 228	2.72	0	Ionic (Ligand Cationic)	false
N52	OD1	ASP- 228	3.93	0	Ionic (Ligand Cationic)	false
C2	CB	THR- 231	4.43	0	Hydrophobic	false
O39	N	THR- 232	3.34	144.52	H-Bond (Protein Donor)	false
C43	CB	THR- 232	4.29	0	Hydrophobic	false
C46	CB	ALA- 335	4.25	0	Hydrophobic	false