scPDB - 2xfy entry

Protein Data Bank Entry:

PDB ID : 2xfy

Resolution :1.210 Å

Experimental Method : X-ray

Deposition Date : 2010-05-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-amylase
ID:	AMYB_HORVU
AC:	P16098
Organism:	Hordeum vulgare
Reign:	Eukaryota
TaxID:	4513
EC Number:	3.2.1.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	12.244
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.977	1086.750

% Hydrophobic	% Polar
36.34	63.66
According to VolSite

Ligand :

HET Code:	ACX
Formula:	C36H60O30
Molecular weight:	972.844 g/mol
DrugBank ID:	DB01909
Buried Surface Area:	26.6 %
Polar Surface area:	474.9 Å2

Number of
H-Bond Acceptors:	30
H-Bond Donors:	18
Rings:	8
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
18.0163	1.37864	21.1704

Binding mode :

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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
C1D	CE2	TYR- 190	4.41	0	Hydrophobic	false
O6E	OE1	GLN- 192	3.46	149.97	H-Bond (Ligand Donor)	false
C6E	CH2	TRP- 196	3.78	0	Hydrophobic	false
C1E	CD2	PHE- 198	3.35	0	Hydrophobic	false
C2E	CE2	PHE- 198	3.51	0	Hydrophobic	false
C5E	CD2	PHE- 198	4.44	0	Hydrophobic	false
C4F	CD1	PHE- 198	4.42	0	Hydrophobic	false
C6F	CB	PHE- 198	3.89	0	Hydrophobic	false
O3E	NE2	HIS- 298	2.84	165.88	H-Bond (Protein Donor)	false
C4E	CZ3	TRP- 299	4.3	0	Hydrophobic	false
O2C	O	ALA- 380	3.04	134.93	H-Bond (Ligand Donor)	false
O3D	O	ALA- 380	2.62	178.79	H-Bond (Ligand Donor)	false
C3D	CD2	LEU- 381	4.38	0	Hydrophobic	false
C3E	CD1	LEU- 381	4.34	0	Hydrophobic	false
C3F	CD1	LEU- 381	3.66	0	Hydrophobic	false
C3B	CG	PRO- 382	3.75	0	Hydrophobic	false
O6D	O	HOH- 2400	3.09	179.95	H-Bond (Protein Donor)	false