scPDB - 4gxs entry

Protein Data Bank Entry:

PDB ID : 4gxs

Resolution :1.960 Å

Experimental Method : X-ray

Deposition Date : 2012-09-04

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
B	3 %
D	97 %

Ligand binding site composition:

B-Factor:	31.909
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.977	1620.000

% Hydrophobic	% Polar
50.42	49.58
According to VolSite

Ligand :

HET Code:	0YS
Formula:	C18H19Cl2N3O9
Molecular weight:	492.264 g/mol
DrugBank ID:	-
Buried Surface Area:	56.65 %
Polar Surface area:	237.02 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-6.34369	47.3142	1.257

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
O7	N	TYR- 61	3.44	127.14	H-Bond (Protein Donor)	false
O8	N	TYR- 61	2.9	174.55	H-Bond (Protein Donor)	false
C6	CE1	TYR- 61	3.79	0	Hydrophobic	false
O7	N	GLY- 62	2.89	170.58	H-Bond (Protein Donor)	false
N	O	PRO- 89	2.78	153.36	H-Bond (Ligand Donor)	false
CL1	CB	THR- 91	3.74	0	Hydrophobic	false
N	OG1	THR- 91	3.29	163.87	H-Bond (Ligand Donor)	false
O1	N	THR- 91	2.74	173.39	H-Bond (Protein Donor)	false
CL1	CG2	THR- 93	3.42	0	Hydrophobic	false
O	CZ	ARG- 96	3.63	0	Ionic (Protein Cationic)	false
O1	CZ	ARG- 96	3.57	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 96	2.86	166.37	H-Bond (Protein Donor)	false
O1	NH1	ARG- 96	2.74	165.56	H-Bond (Protein Donor)	false
C8	CD2	LEU- 138	4.16	0	Hydrophobic	false
C6	CD2	LEU- 138	3.63	0	Hydrophobic	false
CL1	CB	SER- 142	3.93	0	Hydrophobic	false
C15	CB	SER- 142	3.81	0	Hydrophobic	false
O4	N	SER- 142	2.95	165.39	H-Bond (Protein Donor)	false
O2	OG	SER- 142	2.64	136.92	H-Bond (Protein Donor)	false
C13	CG	GLU- 145	4.45	0	Hydrophobic	false
CL	CB	GLU- 145	3.53	0	Hydrophobic	false
N	OE1	GLU- 193	2.93	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 193	3.51	0	Ionic (Ligand Cationic)	false