scPDB - 3h06 entry

Protein Data Bank Entry:

PDB ID : 3h06

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2009-04-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate receptor 2
ID:	GRIA2_RAT
AC:	P19491
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.377
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.783	587.250

% Hydrophobic	% Polar
36.78	63.22
According to VolSite

Ligand :

HET Code:	VBP
Formula:	C15H14N3O6
Molecular weight:	332.288 g/mol
DrugBank ID:	-
Buried Surface Area:	64.76 %
Polar Surface area:	148.52 Å2

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

Mass center Coordinates

X	Y	Z
5.56196	16.0001	9.92163

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
C03	CZ	TYR- 61	3.41	0	Hydrophobic	false
N01	O	PRO- 89	3.33	145.87	H-Bond (Ligand Donor)	false
N01	OG1	THR- 91	2.64	157.93	H-Bond (Ligand Donor)	false
O24	N	THR- 91	2.68	159.82	H-Bond (Protein Donor)	false
O23	CZ	ARG- 96	3.8	0	Ionic (Protein Cationic)	false
O24	CZ	ARG- 96	3.8	0	Ionic (Protein Cationic)	false
O23	NH2	ARG- 96	3.13	159.96	H-Bond (Protein Donor)	false
O24	NH1	ARG- 96	2.92	169.82	H-Bond (Protein Donor)	false
C15	CD2	LEU- 138	3.61	0	Hydrophobic	false
O18	OG1	THR- 143	2.62	161.65	H-Bond (Protein Donor)	false
C16	CB	THR- 174	4.03	0	Hydrophobic	false
C13	CB	LEU- 192	4.13	0	Hydrophobic	false
C12	CB	GLU- 193	4.04	0	Hydrophobic	false
C13	CG	GLU- 193	3.56	0	Hydrophobic	false
C12	CG	MET- 196	3.61	0	Hydrophobic	false
C10	CG	MET- 196	3.79	0	Hydrophobic	false