scPDB - 2hm1 entry

Protein Data Bank Entry:

PDB ID : 2hm1

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-07-10

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:	26.043
Number of residues:	46
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.173	1066.500

% Hydrophobic	% Polar
36.39	63.61
According to VolSite

Ligand :

HET Code:	LIQ
Formula:	C33H43F2N4O5S
Molecular weight:	645.780 g/mol
DrugBank ID:	-
Buried Surface Area:	60.04 %
Polar Surface area:	150.44 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
13.74	-4.26433	18.1722

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
C1A	CD1	LEU- 30	3.34	0	Hydrophobic	false
C16	CD2	LEU- 30	3.54	0	Hydrophobic	false
O4	OD2	ASP- 32	2.59	169.33	H-Bond (Ligand Donor)	false
O4	OD1	ASP- 32	3.49	134.77	H-Bond (Ligand Donor)	false
N23	O	GLY- 34	2.97	155.09	H-Bond (Ligand Donor)	false
C32	CB	SER- 35	3.59	0	Hydrophobic	false
C32	CG1	VAL- 69	3.87	0	Hydrophobic	false
C20	CB	TYR- 71	3.94	0	Hydrophobic	false
C21	CD1	TYR- 71	4.04	0	Hydrophobic	false
C14	CD1	TYR- 71	4.04	0	Hydrophobic	false
C32	CE1	TYR- 71	3.56	0	Hydrophobic	false
F19	CD2	TYR- 71	4.04	0	Hydrophobic	false
C31	CB	THR- 72	4.39	0	Hydrophobic	false
C43	CG2	THR- 72	3.81	0	Hydrophobic	false
C47	CB	GLN- 73	3.53	0	Hydrophobic	false
F19	CD1	PHE- 108	3.28	0	Hydrophobic	false
C3	CD1	ILE- 110	3.94	0	Hydrophobic	false
F17	CD1	ILE- 110	3.44	0	Hydrophobic	false
F17	CH2	TRP- 115	3.32	0	Hydrophobic	false
C14	CD1	ILE- 118	3.95	0	Hydrophobic	false
N23	OD2	ASP- 228	2.6	155.4	H-Bond (Ligand Donor)	false
N23	OD2	ASP- 228	2.6	0	Ionic (Ligand Cationic)	false
N12	O	GLY- 230	3.04	162.92	H-Bond (Ligand Donor)	false
C7	CB	THR- 232	4.33	0	Hydrophobic	false
O1	N	THR- 232	2.93	169.62	H-Bond (Protein Donor)	false