scPDB - 2zjm entry

Protein Data Bank Entry:

PDB ID : 2zjm

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2008-03-07

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:	31.354
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.044	1022.625

% Hydrophobic	% Polar
36.30	63.70
According to VolSite

Ligand :

HET Code:	F1M
Formula:	C24H33ClN3O6S
Molecular weight:	527.053 g/mol
DrugBank ID:	-
Buried Surface Area:	64.33 %
Polar Surface area:	129.77 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
29.4621	38.9246	1.84594

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
C28	CB	GLN- 12	4.33	0	Hydrophobic	false
CL	CB	LEU- 30	3.91	0	Hydrophobic	false
C29	CD1	LEU- 30	3.42	0	Hydrophobic	false
C5	CD1	LEU- 30	3.93	0	Hydrophobic	false
C11	CD1	LEU- 30	3.97	0	Hydrophobic	false
N	OD2	ASP- 32	2.99	143.85	H-Bond (Ligand Donor)	false
N	OD2	ASP- 32	2.99	0	Ionic (Ligand Cationic)	false
CL	CB	ASP- 32	3.91	0	Hydrophobic	false
C8	CB	ASP- 32	3.89	0	Hydrophobic	false
C19	CB	SER- 35	4.03	0	Hydrophobic	false
C19	CD1	TYR- 71	4.02	0	Hydrophobic	false
C17	CG2	THR- 72	3.98	0	Hydrophobic	false
C30	CD1	PHE- 108	3.43	0	Hydrophobic	false
C29	CE1	PHE- 108	3.33	0	Hydrophobic	false
C28	CD1	ILE- 110	4.21	0	Hydrophobic	false
C29	CH2	TRP- 115	3.48	0	Hydrophobic	false
C8	CD1	ILE- 118	3.91	0	Hydrophobic	false
C22	CE1	TYR- 198	3.46	0	Hydrophobic	false
C22	CD1	ILE- 226	3.38	0	Hydrophobic	false
C23	CD1	ILE- 226	4.1	0	Hydrophobic	false
N10	OD2	ASP- 228	2.79	156.55	H-Bond (Ligand Donor)	false
C17	CD	ARG- 235	4.38	0	Hydrophobic	false
O	N	SER- 328	2.55	141.8	H-Bond (Protein Donor)	false
O	OG	SER- 328	3.15	161.58	H-Bond (Protein Donor)	false
C16	CG2	THR- 329	3.54	0	Hydrophobic	false
C17	CG2	VAL- 332	3.84	0	Hydrophobic	false