scPDB - 1lbb entry

Protein Data Bank Entry:

PDB ID : 1lbb

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2002-04-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.200	5.320	5.320	0.120	5.430	2

List of CHEMBLId :

CHEMBL275040

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:	16.970
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.511	418.500

% Hydrophobic	% Polar
46.77	53.23
According to VolSite

Ligand :

HET Code:	KAI
Formula:	C10H14NO4
Molecular weight:	212.222 g/mol
DrugBank ID:	-
Buried Surface Area:	73.3 %
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
9.07407	-29.2947	16.0724

Binding mode :

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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
CD2	CE1	TYR- 61	3.6	0	Hydrophobic	false
CG	CZ	TYR- 61	3.84	0	Hydrophobic	false
N	O	PRO- 89	2.93	128.77	H-Bond (Ligand Donor)	false
O	N	THR- 91	3.14	168.09	H-Bond (Protein Donor)	false
O	NH1	ARG- 96	2.96	165	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 96	3.11	143.22	H-Bond (Protein Donor)	false
O	CZ	ARG- 96	3.69	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 96	3.76	0	Ionic (Protein Cationic)	false
CD2	CD1	LEU- 138	3.56	0	Hydrophobic	false
CB1	CD1	LEU- 138	3.64	0	Hydrophobic	false
OXT	OG	SER- 142	2.72	153.46	H-Bond (Protein Donor)	false
OXT	N	SER- 142	2.99	163.3	H-Bond (Protein Donor)	false
OD1	OG1	THR- 143	2.62	163.64	H-Bond (Protein Donor)	false
OD2	N	THR- 143	2.93	173.03	H-Bond (Protein Donor)	false
N	OE1	GLU- 193	2.9	161.35	H-Bond (Ligand Donor)	false
N	OE2	GLU- 193	3.48	132.16	H-Bond (Ligand Donor)	false
N	OE1	GLU- 193	2.9	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 193	3.48	0	Ionic (Ligand Cationic)	false
CB1	CG	GLU- 193	4.06	0	Hydrophobic	false
CB1	CE	MET- 196	4.44	0	Hydrophobic	false
CG	CE	MET- 196	4.48	0	Hydrophobic	false