scPDB - 3h03 entry

Protein Data Bank Entry:

PDB ID : 3h03

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-04-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate receptor 2
ID:	GRIA2_RAT
AC:	P19491
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:	8.447
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.277	631.125

% Hydrophobic	% Polar
40.11	59.89
According to VolSite

Ligand :

HET Code:	UBP
Formula:	C10H12N3O6
Molecular weight:	270.219 g/mol
DrugBank ID:	-
Buried Surface Area:	66.2 %
Polar Surface area:	148.52 Å2

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

Mass center Coordinates

X	Y	Z
24.1848	28.9668	27.3577

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
C7	CE1	TYR- 61	3.57	0	Hydrophobic	false
N8	O	PRO- 89	3.02	158.35	H-Bond (Ligand Donor)	false
N8	OG1	THR- 91	2.76	145.13	H-Bond (Ligand Donor)	false
O91	N	THR- 91	2.78	167.6	H-Bond (Protein Donor)	false
O91	CZ	ARG- 96	3.55	0	Ionic (Protein Cationic)	false
O92	CZ	ARG- 96	3.73	0	Ionic (Protein Cationic)	false
O91	NH2	ARG- 96	3.47	128.3	H-Bond (Protein Donor)	false
O91	NH1	ARG- 96	2.78	160.13	H-Bond (Protein Donor)	false
O92	NH2	ARG- 96	2.88	178.82	H-Bond (Protein Donor)	false
C3	CG2	THR- 174	4.2	0	Hydrophobic	false
O1	OG1	THR- 174	2.73	165.02	H-Bond (Protein Donor)	false
O1	OH	TYR- 190	2.85	147.93	H-Bond (Protein Donor)	false
C3	CB	LEU- 192	4.44	0	Hydrophobic	false
N8	OE2	GLU- 193	3.79	0	Ionic (Ligand Cationic)	false
N8	OE1	GLU- 193	3.1	0	Ionic (Ligand Cationic)	false
N8	OE1	GLU- 193	3.1	147.36	H-Bond (Ligand Donor)	false
C1	CG	GLU- 193	3.94	0	Hydrophobic	false
C3	CB	GLU- 193	4.2	0	Hydrophobic	false
O3	N	GLU- 193	3.29	159.76	H-Bond (Protein Donor)	false
C3	CB	MET- 196	3.82	0	Hydrophobic	false