scPDB - 3b7d entry

Protein Data Bank Entry:

PDB ID : 3b7d

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-10-30

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
A	100 %

Ligand binding site composition:

B-Factor:	21.836
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.145	992.250

% Hydrophobic	% Polar
48.30	51.70
According to VolSite

Ligand :

HET Code:	CNI
Formula:	C9H2N4O4
Molecular weight:	230.137 g/mol
DrugBank ID:	-
Buried Surface Area:	69.81 %
Polar Surface area:	128.46 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	2
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
-30.2131	14.4711	-39.1787

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
C4	CZ	TYR- 61	3.4	0	Hydrophobic	false
C6	CB	PRO- 89	4.34	0	Hydrophobic	false
N2	O	PRO- 89	2.84	164.99	H-Bond (Ligand Donor)	false
O2	N	THR- 91	2.88	176.34	H-Bond (Protein Donor)	false
O1	NH2	ARG- 96	2.99	160.16	H-Bond (Protein Donor)	false
O2	NH2	ARG- 96	3.45	123.89	H-Bond (Protein Donor)	false
O2	NH1	ARG- 96	2.79	143.54	H-Bond (Protein Donor)	false
O3	OG1	THR- 174	3.46	124.61	H-Bond (Protein Donor)	false
C5	CG	GLU- 193	4.36	0	Hydrophobic	false
C8	CG	GLU- 193	4.21	0	Hydrophobic	false