scPDB - 2qs4 entry

Protein Data Bank Entry:

PDB ID : 2qs4

Resolution :1.580 Å

Experimental Method : X-ray

Deposition Date : 2007-07-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate receptor ionotropic, kainate 1
ID:	GRIK1_RAT
AC:	P22756
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	8.025
Number of residues:	32
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.967	1208.250

% Hydrophobic	% Polar
32.68	67.32
According to VolSite

Ligand :

HET Code:	LY5
Formula:	C16H24F2N2O4
Molecular weight:	346.370 g/mol
DrugBank ID:	-
Buried Surface Area:	66.4 %
Polar Surface area:	101.31 Å2

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

Mass center Coordinates

X	Y	Z
-19.4352	23.5024	-15.2812

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
C9	CG	GLU- 13	4.14	0	Hydrophobic	false
C9	CE1	TYR- 16	4.47	0	Hydrophobic	false
C2	CE1	TYR- 61	3.53	0	Hydrophobic	false
C5	CZ	TYR- 61	3.69	0	Hydrophobic	false
N1	O	PRO- 88	2.7	139.92	H-Bond (Ligand Donor)	false
C9	CG	PRO- 88	4.18	0	Hydrophobic	false
N1	OG1	THR- 90	2.82	165.13	H-Bond (Ligand Donor)	false
O2	N	THR- 90	2.85	177.04	H-Bond (Protein Donor)	false
O1	NH2	ARG- 95	2.96	159.92	H-Bond (Protein Donor)	false
O1	NH1	ARG- 95	3.5	133.36	H-Bond (Protein Donor)	false
O2	NH1	ARG- 95	2.76	156.52	H-Bond (Protein Donor)	false
O1	CZ	ARG- 95	3.66	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 95	3.57	0	Ionic (Protein Cationic)	false
C14	CG2	VAL- 137	3.75	0	Hydrophobic	false
O4	OG	SER- 141	2.8	148.44	H-Bond (Protein Donor)	false
O4	N	THR- 142	3.11	157.28	H-Bond (Protein Donor)	false
O4	OG1	THR- 142	3.43	123.94	H-Bond (Protein Donor)	false
O3	OG1	THR- 142	2.54	167.16	H-Bond (Protein Donor)	false
F1	CB	SER- 173	3.42	0	Hydrophobic	false
F2	CE	MET- 189	3.4	0	Hydrophobic	false
O3	N	GLU- 190	2.75	142.22	H-Bond (Protein Donor)	false
C9	CZ	TYR- 216	4.49	0	Hydrophobic	false