scPDB - 2qs3 entry

Protein Data Bank Entry:

PDB ID : 2qs3

Resolution :1.760 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
B	100 %

Ligand binding site composition:

B-Factor:	30.571
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.855	988.875

% Hydrophobic	% Polar
35.15	64.85
According to VolSite

Ligand :

HET Code:	UBE
Formula:	C20H18N3O6S
Molecular weight:	428.438 g/mol
DrugBank ID:	-
Buried Surface Area:	50.54 %
Polar Surface area:	176.76 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-53.9308	-4.39713	15.3669

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
C13	CG	GLU- 13	3.77	0	Hydrophobic	false
C13	CE1	TYR- 16	4.07	0	Hydrophobic	false
C7	CD1	TYR- 61	3.68	0	Hydrophobic	false
C13	CB	PRO- 88	3.79	0	Hydrophobic	false
N9	O	PRO- 88	2.93	162.63	H-Bond (Ligand Donor)	false
N9	OG1	THR- 90	3.05	171.37	H-Bond (Ligand Donor)	false
O11	N	THR- 90	2.81	176.16	H-Bond (Protein Donor)	false
O11	NH2	ARG- 95	3.46	127.17	H-Bond (Protein Donor)	false
O11	NH1	ARG- 95	2.7	163.29	H-Bond (Protein Donor)	false
O12	NH2	ARG- 95	2.78	166.98	H-Bond (Protein Donor)	false
O11	CZ	ARG- 95	3.51	0	Ionic (Protein Cationic)	false
O12	CZ	ARG- 95	3.59	0	Ionic (Protein Cationic)	false
S20	CB	VAL- 137	3.62	0	Hydrophobic	false
C26	CG1	VAL- 137	4	0	Hydrophobic	false
O24	OG1	THR- 142	2.69	163.39	H-Bond (Protein Donor)	false
O23	N	THR- 142	2.74	164.94	H-Bond (Protein Donor)	false
O23	OG1	THR- 142	3.19	134.53	H-Bond (Protein Donor)	false
C29	CB	ASN- 172	3.93	0	Hydrophobic	false
C16	CG	GLU- 190	4.15	0	Hydrophobic	false
O23	O	HOH- 672	2.53	123.85	H-Bond (Protein Donor)	false