scPDB - 3rt8 entry

Protein Data Bank Entry:

PDB ID : 3rt8

Resolution :2.430 Å

Experimental Method : X-ray

Deposition Date : 2011-05-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.350	6.350	6.350	0.000	6.350	1

List of CHEMBLId :

CHEMBL121388

Binding Site :

Uniprot Annotation

Name:	Glutamate receptor 3
ID:	GRIA3_RAT
AC:	P19492
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:	32.414
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.768	705.375

% Hydrophobic	% Polar
53.11	46.89
According to VolSite

Ligand :

HET Code:	CWD
Formula:	C7H8ClN3O4
Molecular weight:	233.609 g/mol
DrugBank ID:	-
Buried Surface Area:	75.69 %
Polar Surface area:	117.18 Å2

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

Mass center Coordinates

X	Y	Z
-19.8854	-1.20707	-19.8581

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
C7	CD1	TYR- 61	3.57	0	Hydrophobic	false
N8	O	PRO- 89	3.16	145.71	H-Bond (Ligand Donor)	false
N8	OG1	THR- 91	2.85	156.34	H-Bond (Ligand Donor)	false
O91	N	THR- 91	2.97	166.82	H-Bond (Protein Donor)	false
O91	CZ	ARG- 96	3.55	0	Ionic (Protein Cationic)	false
O92	CZ	ARG- 96	3.64	0	Ionic (Protein Cationic)	false
O91	NH1	ARG- 96	2.87	160.38	H-Bond (Protein Donor)	false
O91	NH2	ARG- 96	3.36	134.1	H-Bond (Protein Donor)	false
O92	NH2	ARG- 96	2.76	156.49	H-Bond (Protein Donor)	false
C7	CD2	LEU- 138	4.45	0	Hydrophobic	false
O92	N	SER- 142	3.27	153.59	H-Bond (Protein Donor)	false
O2	N	THR- 143	3.39	178.5	H-Bond (Protein Donor)	false
CL5	CG2	THR- 174	4.23	0	Hydrophobic	false
O4	N	GLU- 193	3.06	159.83	H-Bond (Protein Donor)	false
CL5	CB	GLU- 193	4.24	0	Hydrophobic	false
N8	OE1	GLU- 193	3.06	166.61	H-Bond (Ligand Donor)	false
N8	OE2	GLU- 193	3.13	124.94	H-Bond (Ligand Donor)	false
N8	OE1	GLU- 193	3.06	0	Ionic (Ligand Cationic)	false
N8	OE2	GLU- 193	3.13	0	Ionic (Ligand Cationic)	false
CL5	CB	MET- 196	4.05	0	Hydrophobic	false
O4	O	HOH- 262	2.71	160.56	H-Bond (Protein Donor)	false