scPDB - 3s2v entry

Protein Data Bank Entry:

PDB ID : 3s2v

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-05-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.800	6.800	6.800	0.000	6.800	1

List of CHEMBLId :

CHEMBL1738726

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:	18.526
Number of residues:	37
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.368	526.500

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	3HU
Formula:	C15H12N3O6S2
Molecular weight:	394.402 g/mol
DrugBank ID:	-
Buried Surface Area:	63.82 %
Polar Surface area:	205 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:	6

Mass center Coordinates

X	Y	Z
45.5196	57.3023	4.74831

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
SAN	CG	GLU- 13	3.74	0	Hydrophobic	false
CB	CZ	TYR- 61	3.63	0	Hydrophobic	false
N	O	PRO- 88	3.01	171.46	H-Bond (Ligand Donor)	false
SAN	CG	PRO- 88	3.38	0	Hydrophobic	false
N	OG1	THR- 90	2.82	164.8	H-Bond (Ligand Donor)	false
O	N	THR- 90	2.87	171.75	H-Bond (Protein Donor)	false
O	CZ	ARG- 95	3.47	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 95	3.58	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 95	3.42	126.25	H-Bond (Protein Donor)	false
O	NH1	ARG- 95	2.69	159.11	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 95	2.75	172.42	H-Bond (Protein Donor)	false
SAO	CG2	VAL- 137	3.33	0	Hydrophobic	false
OAB	OG1	THR- 142	2.63	161.69	H-Bond (Protein Donor)	false
OAF	N	THR- 142	3.06	145.36	H-Bond (Protein Donor)	false
OAF	OG1	THR- 142	2.88	128.72	H-Bond (Protein Donor)	false
CAL	CG	MET- 189	4.45	0	Hydrophobic	false
N	OE2	GLU- 190	3.17	159.13	H-Bond (Ligand Donor)	false
N	OE2	GLU- 190	3.17	0	Ionic (Ligand Cationic)	false
CAL	CB	GLU- 190	3.58	0	Hydrophobic	false
OAD	OG	SER- 193	2.65	154.02	H-Bond (Protein Donor)	false
OAF	O	HOH- 263	2.59	138.34	H-Bond (Protein Donor)	false
OAB	O	HOH- 434	3.09	135.45	H-Bond (Protein Donor)	false