scPDB - 3dm6 entry

Protein Data Bank Entry:

PDB ID : 3dm6

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2008-06-30

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	98 %
B	2 %

Ligand binding site composition:

B-Factor:	50.191
Number of residues:	54
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.111	894.375

% Hydrophobic	% Polar
41.51	58.49
According to VolSite

Ligand :

HET Code:	757
Formula:	C42H43F2N5O12S
Molecular weight:	879.879 g/mol
DrugBank ID:	-
Buried Surface Area:	60.69 %
Polar Surface area:	271.87 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	4
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
0.574081	15.099	36.3381

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
C9	CD1	LEU- 30	3.99	0	Hydrophobic	false
C38	CD2	LEU- 30	4.22	0	Hydrophobic	false
O42	OD1	ASP- 32	2.78	164.99	H-Bond (Ligand Donor)	false
N46	O	GLY- 34	2.8	154.71	H-Bond (Ligand Donor)	false
C50	CB	SER- 35	3.4	0	Hydrophobic	false
C49	CG1	VAL- 69	3.75	0	Hydrophobic	false
N53	O	PRO- 70	2.7	167.85	H-Bond (Ligand Donor)	false
C31	CD1	TYR- 71	3.61	0	Hydrophobic	false
C41	CD1	TYR- 71	4.05	0	Hydrophobic	false
C34	CB	TYR- 71	3.41	0	Hydrophobic	false
C22	CG2	THR- 72	3.62	0	Hydrophobic	false
C15	CB	THR- 72	4.16	0	Hydrophobic	false
O45	N	THR- 72	3.29	154.05	H-Bond (Protein Donor)	false
O64	OG1	THR- 72	2.87	132.49	H-Bond (Protein Donor)	false
O19	N	GLN- 73	3.36	158.09	H-Bond (Protein Donor)	false
C36	CB	GLN- 73	3.6	0	Hydrophobic	false
C15	CG	GLN- 73	3.33	0	Hydrophobic	false
F40	CD1	PHE- 108	3.66	0	Hydrophobic	false
C9	CD1	ILE- 110	3.99	0	Hydrophobic	false
F39	CD1	ILE- 110	3.34	0	Hydrophobic	false
C9	CZ2	TRP- 115	4.12	0	Hydrophobic	false
F39	CZ2	TRP- 115	3.78	0	Hydrophobic	false
C31	CD1	ILE- 118	3.86	0	Hydrophobic	false
C50	CD1	ILE- 126	3.39	0	Hydrophobic	false
C50	CE1	TYR- 198	4.2	0	Hydrophobic	false
O52	OH	TYR- 198	2.77	150.05	H-Bond (Protein Donor)	false
O42	OD2	ASP- 228	2.54	151.89	H-Bond (Protein Donor)	false
N8	O	GLY- 230	3.27	138.44	H-Bond (Ligand Donor)	false
N29	O	GLY- 230	3.21	175.64	H-Bond (Ligand Donor)	false
C16	CB	THR- 231	4.31	0	Hydrophobic	false
C14	CG2	THR- 231	3.64	0	Hydrophobic	false
C13	CB	THR- 232	4.27	0	Hydrophobic	false
C1	CB	THR- 232	4	0	Hydrophobic	false
O26	N	THR- 232	3.31	124.81	H-Bond (Protein Donor)	false
O26	N	ASN- 233	2.99	153.7	H-Bond (Protein Donor)	false
C22	CD	ARG- 235	3.97	0	Hydrophobic	false
C3	CB	ALA- 335	3.67	0	Hydrophobic	false