scPDB - 2wky entry

Protein Data Bank Entry:

PDB ID : 2wky

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2009-06-18

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:	21.998
Number of residues:	32
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.653	540.000

% Hydrophobic	% Polar
43.75	56.25
According to VolSite

Ligand :

HET Code:	IBC
Formula:	C11H13N2O4
Molecular weight:	237.232 g/mol
DrugBank ID:	DB04152
Buried Surface Area:	73.52 %
Polar Surface area:	116.86 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
32.8705	-0.244882	77.047

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
C6	CG	GLU- 13	3.89	0	Hydrophobic	false
C9	CD2	TYR- 61	3.91	0	Hydrophobic	false
C6	CZ	TYR- 61	4.29	0	Hydrophobic	false
N2	O	PRO- 88	2.77	144.76	H-Bond (Ligand Donor)	false
C6	CG	PRO- 88	4.38	0	Hydrophobic	false
O3	N	THR- 90	2.75	171.04	H-Bond (Protein Donor)	false
N2	OG1	THR- 90	2.98	160.29	H-Bond (Ligand Donor)	false
O4	NH1	ARG- 95	3.39	129.57	H-Bond (Protein Donor)	false
O4	NH2	ARG- 95	2.8	155.53	H-Bond (Protein Donor)	false
O3	NH1	ARG- 95	2.64	169.24	H-Bond (Protein Donor)	false
O4	CZ	ARG- 95	3.52	0	Ionic (Protein Cationic)	false
O3	CZ	ARG- 95	3.52	0	Ionic (Protein Cationic)	false
O4	N	SER- 141	2.85	136.52	H-Bond (Protein Donor)	false
C8	CG	MET- 189	4.13	0	Hydrophobic	false
N2	OE2	GLU- 190	3.65	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 190	2.94	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 190	2.94	135.96	H-Bond (Ligand Donor)	false
C8	CB	GLU- 190	3.93	0	Hydrophobic	false
O1	N	GLU- 190	3.22	165.33	H-Bond (Protein Donor)	false
C8	CB	SER- 193	3.89	0	Hydrophobic	false
O2	O	HOH- 2083	2.9	179.96	H-Bond (Protein Donor)	false