scPDB - 4b72 entry

Protein Data Bank Entry:

PDB ID : 4b72

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2012-08-16

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:	23.783
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.208	1323.000

% Hydrophobic	% Polar
38.52	61.48
According to VolSite

Ligand :

HET Code:	2FB
Formula:	C23H20N5OS
Molecular weight:	414.503 g/mol
DrugBank ID:	-
Buried Surface Area:	60.67 %
Polar Surface area:	116.13 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
5.76773	1.63337	-20.5146

Binding mode :

What is Poseview ?

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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
C23	CD2	LEU- 30	4.19	0	Hydrophobic	false
N8	OD2	ASP- 32	2.69	152.8	H-Bond (Ligand Donor)	false
N10	OD2	ASP- 32	3.46	121.05	H-Bond (Ligand Donor)	false
N10	OD1	ASP- 32	2.87	171.54	H-Bond (Ligand Donor)	false
C9	OD2	ASP- 32	3.41	0	Ionic (Ligand Cationic)	false
C9	OD1	ASP- 32	3.66	0	Ionic (Ligand Cationic)	false
C15	CB	SER- 35	3.58	0	Hydrophobic	false
C18	CB	ASN- 37	4.26	0	Hydrophobic	false
C13	CG1	VAL- 69	4.46	0	Hydrophobic	false
C18	CG1	VAL- 69	4.25	0	Hydrophobic	false
C13	CB	TYR- 71	4.36	0	Hydrophobic	false
C1	CG2	THR- 72	4.26	0	Hydrophobic	false
O17	NE1	TRP- 76	2.9	171.68	H-Bond (Protein Donor)	false
C18	CZ2	TRP- 76	3.7	0	Hydrophobic	false
C16	CD1	ILE- 118	3.82	0	Hydrophobic	false
C20	CD1	ILE- 118	3.56	0	Hydrophobic	false
C18	CG	ARG- 128	4.26	0	Hydrophobic	false
C9	OD2	ASP- 228	3.94	0	Ionic (Ligand Cationic)	false
N10	OD2	ASP- 228	2.82	153.71	H-Bond (Ligand Donor)	false