scPDB - 3ptq entry

Protein Data Bank Entry:

PDB ID : 3ptq

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2010-12-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-glucosidase 12
ID:	BGL12_ORYSI
AC:	B8AVF0
Organism:	Oryza sativa subsp. indica
Reign:	Eukaryota
TaxID:	39946
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.782
Number of residues:	34
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.242	428.625

% Hydrophobic	% Polar
50.39	49.61
According to VolSite

Ligand :

HET Code:	NFG
Formula:	C12H13FN2O9
Molecular weight:	348.238 g/mol
DrugBank ID:	DB02658
Buried Surface Area:	74.35 %
Polar Surface area:	170.78 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-30.1357	-8.80896	-23.1975

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
O3	OE1	GLN- 29	2.75	132.56	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 29	2.71	174.6	H-Bond (Protein Donor)	false
O3	NE2	HIS- 133	3.08	157.58	H-Bond (Protein Donor)	false
C2	CH2	TRP- 134	3.88	0	Hydrophobic	false
F	CZ2	TRP- 134	4.22	0	Hydrophobic	false
F	CG	GLU- 179	3.68	0	Hydrophobic	false
C13	CG2	THR- 182	4.1	0	Hydrophobic	false
C16	CG2	THR- 182	3.96	0	Hydrophobic	false
C1	CE2	TYR- 322	4.23	0	Hydrophobic	false
C5	CZ	TYR- 322	3.93	0	Hydrophobic	false
C6	CZ2	TRP- 365	4.39	0	Hydrophobic	false
C3	CZ2	TRP- 442	4.01	0	Hydrophobic	false
C5	CE2	TRP- 442	3.86	0	Hydrophobic	false
O4	OE1	GLU- 449	2.54	157.39	H-Bond (Ligand Donor)	false
O6	OE2	GLU- 449	2.63	165.48	H-Bond (Ligand Donor)	false
O3	NE1	TRP- 450	3.12	157.58	H-Bond (Protein Donor)	false
C6	CZ	PHE- 458	3.63	0	Hydrophobic	false