scPDB - 2j7c entry

Protein Data Bank Entry:

PDB ID : 2j7c

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2006-10-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-glucosidase A
ID:	BGLA_THEMA
AC:	Q08638
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	3.2.1.21

Chains:

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

Ligand binding site composition:

B-Factor:	23.120
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.937	985.500

% Hydrophobic	% Polar
40.75	59.25
According to VolSite

Ligand :

HET Code:	IDE
Formula:	C15H20N3O4
Molecular weight:	306.337 g/mol
DrugBank ID:	DB04712
Buried Surface Area:	67.32 %
Polar Surface area:	112.02 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-0.874727	9.04091	10.42

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
O4B	NE2	GLN- 20	2.87	173.4	H-Bond (Protein Donor)	false
O3B	OE1	GLN- 20	2.71	133.05	H-Bond (Ligand Donor)	false
O3B	NE2	HIS- 121	2.98	152.37	H-Bond (Protein Donor)	false
O2B	NE2	HIS- 121	3.29	122.06	H-Bond (Protein Donor)	false
C2B	CH2	TRP- 122	3.96	0	Hydrophobic	false
O2B	ND2	ASN- 165	2.99	153.33	H-Bond (Protein Donor)	false
C5	CG1	VAL- 169	3.95	0	Hydrophobic	false
C6	CG2	VAL- 169	3.7	0	Hydrophobic	false
C6B	CE2	TYR- 295	4.16	0	Hydrophobic	false
C5B	CZ	TYR- 295	3.96	0	Hydrophobic	false
C7	CD1	TYR- 295	3.51	0	Hydrophobic	false
C6B	CH2	TRP- 324	4.2	0	Hydrophobic	false
O2B	OE1	GLU- 351	2.89	151.2	H-Bond (Ligand Donor)	false
C3B	CZ2	TRP- 398	3.71	0	Hydrophobic	false
C4B	CE2	TRP- 398	3.86	0	Hydrophobic	false
O6B	OE2	GLU- 405	2.66	167	H-Bond (Ligand Donor)	false
O4B	OE1	GLU- 405	2.52	153.61	H-Bond (Ligand Donor)	false
O3B	NE1	TRP- 406	2.77	170.09	H-Bond (Protein Donor)	false
C6B	CZ	PHE- 414	3.37	0	Hydrophobic	false
O4B	O	HOH- 2306	3.33	129.02	H-Bond (Protein Donor)	false