scPDB - 3c36 entry

Protein Data Bank Entry:

PDB ID : 3c36

Resolution :1.680 Å

Experimental Method : X-ray

Deposition Date : 2008-01-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.090	5.090	5.090	0.000	5.090	3

List of CHEMBLId :

CHEMBL279561

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:	15.281
Number of residues:	33
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.416	489.375

% Hydrophobic	% Polar
40.69	59.31
According to VolSite

Ligand :

HET Code:	KAI
Formula:	C10H14NO4
Molecular weight:	212.222 g/mol
DrugBank ID:	-
Buried Surface Area:	66.51 %
Polar Surface area:	96.87 Å2

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

Mass center Coordinates

X	Y	Z
-1.31733	32.5543	44.4377

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
CD1	CG	GLU- 13	4.11	0	Hydrophobic	false
CD2	CE1	TYR- 61	3.52	0	Hydrophobic	false
CG	CE1	TYR- 61	3.6	0	Hydrophobic	false
CG2	CE1	TYR- 61	3.56	0	Hydrophobic	false
N	O	PRO- 88	2.91	131.86	H-Bond (Ligand Donor)	false
O	N	THR- 90	3.03	177.39	H-Bond (Protein Donor)	false
O	CZ	ARG- 95	3.63	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 95	3.55	0	Ionic (Protein Cationic)	false
O	NH1	ARG- 95	2.84	164.23	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 95	2.88	141.39	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 95	3.34	127.75	H-Bond (Protein Donor)	false
CD2	CG1	VAL- 137	4.04	0	Hydrophobic	false
OXT	N	SER- 141	2.96	148.56	H-Bond (Protein Donor)	false
OXT	OG	SER- 141	2.75	157.82	H-Bond (Protein Donor)	false
OD1	OG1	THR- 142	2.68	166.85	H-Bond (Protein Donor)	false
OD2	N	THR- 142	2.97	173.48	H-Bond (Protein Donor)	false
OD2	OG1	THR- 142	3.44	121.89	H-Bond (Protein Donor)	false
N	OE2	GLU- 190	3.6	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 190	2.85	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 190	2.85	160.13	H-Bond (Ligand Donor)	false
OD2	O	HOH- 408	2.79	179.96	H-Bond (Protein Donor)	false
OD1	O	HOH- 411	3	164.55	H-Bond (Protein Donor)	false