scPDB - 2ntr entry

Protein Data Bank Entry:

PDB ID : 2ntr

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2006-11-08

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:	22.020
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.615	681.750

% Hydrophobic	% Polar
28.71	71.29
According to VolSite

Ligand :

HET Code:	L00
Formula:	C26H36ClN6O4S
Molecular weight:	564.120 g/mol
DrugBank ID:	-
Buried Surface Area:	68 %
Polar Surface area:	137.67 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
30.1859	42.8189	1.31121

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
C27	CD1	LEU- 30	3.43	0	Hydrophobic	false
N6	OD2	ASP- 32	3.4	132.45	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 32	2.56	164.18	H-Bond (Ligand Donor)	false
N6	OD2	ASP- 32	3.4	0	Ionic (Ligand Cationic)	false
N6	OD1	ASP- 32	2.56	0	Ionic (Ligand Cationic)	false
C21	CB	SER- 35	4.21	0	Hydrophobic	false
C21	CD1	TYR- 71	3.79	0	Hydrophobic	false
C22	CG	TYR- 71	3.71	0	Hydrophobic	false
C25	CB	TYR- 71	4	0	Hydrophobic	false
CL	CG2	THR- 72	3.59	0	Hydrophobic	false
C24	CG	GLN- 73	4.39	0	Hydrophobic	false
C11	CB	GLN- 73	3.78	0	Hydrophobic	false
N4	N	GLN- 73	3.4	130.43	H-Bond (Protein Donor)	false
O1	NE2	GLN- 73	2.94	166.99	H-Bond (Protein Donor)	false
C23	CD1	ILE- 110	4.46	0	Hydrophobic	false
C1	CD1	ILE- 110	3.72	0	Hydrophobic	false
C4	CD1	ILE- 110	3.62	0	Hydrophobic	false
C7	CD1	ILE- 110	4.12	0	Hydrophobic	false
C27	CD1	ILE- 118	3.98	0	Hydrophobic	false
N6	OD1	ASP- 228	3.36	129.86	H-Bond (Ligand Donor)	false
N6	OD2	ASP- 228	2.93	157.49	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 228	3.36	0	Ionic (Ligand Cationic)	false
N6	OD2	ASP- 228	2.93	0	Ionic (Ligand Cationic)	false
N6	O	GLY- 230	3.01	152.28	H-Bond (Ligand Donor)	false
C11	CB	THR- 231	4.47	0	Hydrophobic	false
C12	CG2	THR- 231	4.11	0	Hydrophobic	false
C15	CB	THR- 232	4.4	0	Hydrophobic	false
C2	CB	THR- 232	4.09	0	Hydrophobic	false
O2	N	ASN- 233	3.07	178.15	H-Bond (Protein Donor)	false
CL	CD	ARG- 235	3.88	0	Hydrophobic	false