scPDB - 1lbc entry

Protein Data Bank Entry:

PDB ID : 1lbc

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2002-04-02

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	65 %
C	35 %

Ligand binding site composition:

B-Factor:	15.131
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.697	1846.125

% Hydrophobic	% Polar
46.44	53.56
According to VolSite

Ligand :

HET Code:	CYZ
Formula:	C14H16ClN3O4S2
Molecular weight:	389.878 g/mol
DrugBank ID:	DB00606
Buried Surface Area:	63.69 %
Polar Surface area:	135.11 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
60.6957	31.1183	42.1939

Binding mode :

What is Poseview ?

2D View
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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	CG2	ILE- 92	3.71	0	Hydrophobic	false
C7	CB	LYS- 104	3.5	0	Hydrophobic	false
C2	CG	PRO- 105	4.32	0	Hydrophobic	false
N1	O	PRO- 105	2.85	126.87	H-Bond (Ligand Donor)	false
C11	CB	SER- 108	4.18	0	Hydrophobic	false
O2	OG	SER- 108	2.74	146.66	H-Bond (Protein Donor)	false
O3	N	SER- 108	3.11	172.58	H-Bond (Protein Donor)	false
C14	CB	SER- 217	4.23	0	Hydrophobic	false
C12	CB	SER- 217	4.06	0	Hydrophobic	false
C9	CB	SER- 217	4.2	0	Hydrophobic	false
C6	CB	LYS- 218	4.36	0	Hydrophobic	false
C6	CD1	LEU- 239	3.57	0	Hydrophobic	false
C7	CD1	LEU- 239	3.4	0	Hydrophobic	false
N2	OG	SER- 242	2.95	166.65	H-Bond (Ligand Donor)	false
C14	CB	SER- 242	4.25	0	Hydrophobic	false
C6	CB	SER- 242	3.81	0	Hydrophobic	false
C14	CD1	LEU- 247	3.69	0	Hydrophobic	false
CL	CB	LEU- 247	3.32	0	Hydrophobic	false
CL	CB	ASP- 248	3.61	0	Hydrophobic	false