scPDB - 4dpf entry

Protein Data Bank Entry:

PDB ID : 4dpf

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2012-02-13

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
A	100 %

Ligand binding site composition:

B-Factor:	16.926
Number of residues:	48
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.093	1107.000

% Hydrophobic	% Polar
38.11	61.89
According to VolSite

Ligand :

HET Code:	0LG
Formula:	C35H45N4O6S
Molecular weight:	649.820 g/mol
DrugBank ID:	-
Buried Surface Area:	60.8 %
Polar Surface area:	150.03 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
5.87465	0.721435	-17.3895

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
C31	CG	GLN- 60	3.42	0	Hydrophobic	false
C35	CG	LEU- 78	4.49	0	Hydrophobic	false
O21	OD2	ASP- 80	2.61	160.99	H-Bond (Ligand Donor)	false
N20	O	GLY- 82	3.04	144.89	H-Bond (Ligand Donor)	false
C44	CB	SER- 83	4.18	0	Hydrophobic	false
C46	CG1	VAL- 117	3.96	0	Hydrophobic	false
C18	CD1	TYR- 119	4.05	0	Hydrophobic	false
C22	CD1	TYR- 119	4.13	0	Hydrophobic	false
C44	CD1	TYR- 119	4.26	0	Hydrophobic	false
C10	CG2	THR- 120	3.73	0	Hydrophobic	false
C5	CB	THR- 120	4.12	0	Hydrophobic	false
C10	CG	GLN- 121	4.24	0	Hydrophobic	false
C5	CG	GLN- 121	3.74	0	Hydrophobic	false
O15	N	GLN- 121	3.28	168.89	H-Bond (Protein Donor)	false
C35	CE1	PHE- 156	4.4	0	Hydrophobic	false
C26	CD1	ILE- 158	3.64	0	Hydrophobic	false
C28	CD1	ILE- 158	3.55	0	Hydrophobic	false
C26	CZ2	TRP- 163	4.04	0	Hydrophobic	false
C22	CD1	ILE- 166	3.8	0	Hydrophobic	false
C35	CD1	ILE- 166	3.92	0	Hydrophobic	false
C45	CD1	ILE- 174	3.87	0	Hydrophobic	false
C45	CE1	TYR- 246	4.02	0	Hydrophobic	false
N20	OD1	ASP- 276	3.95	0	Ionic (Ligand Cationic)	false
N20	OD2	ASP- 276	2.68	0	Ionic (Ligand Cationic)	false
N20	OD2	ASP- 276	2.68	163.4	H-Bond (Ligand Donor)	false
N16	O	GLY- 278	2.96	165.31	H-Bond (Ligand Donor)	false
C4	CB	THR- 279	4.28	0	Hydrophobic	false
C6	CG2	THR- 279	3.87	0	Hydrophobic	false
O24	N	THR- 280	3.12	121.09	H-Bond (Protein Donor)	false
O24	OG1	THR- 280	2.61	161.93	H-Bond (Protein Donor)	false
O13	N	ASN- 281	3.11	151.2	H-Bond (Protein Donor)	false
C10	CD	ARG- 283	4.27	0	Hydrophobic	false
O14	O	HOH- 622	3.2	154.31	H-Bond (Protein Donor)	false