scPDB - 4lz8 entry

Protein Data Bank Entry:

PDB ID : 4lz8

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2013-07-31

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	58 %
C	42 %

Ligand binding site composition:

B-Factor:	16.757
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.399	428.625

% Hydrophobic	% Polar
33.07	66.93
According to VolSite

Ligand :

HET Code:	1YX
Formula:	C19H27FN4O4S
Molecular weight:	426.505 g/mol
DrugBank ID:	-
Buried Surface Area:	67.3 %
Polar Surface area:	108.48 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
61.0496	27.5488	44.2189

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
C2	CB	LYS- 493	4.25	0	Hydrophobic	false
C3	CG	LYS- 493	3.73	0	Hydrophobic	false
C19	CB	LYS- 493	4.31	0	Hydrophobic	false
N1	O	PRO- 494	2.88	173.37	H-Bond (Ligand Donor)	false
N4	O	PRO- 494	2.83	134.98	H-Bond (Ligand Donor)	false
F1	CB	PRO- 494	3.54	0	Hydrophobic	false
C14	CB	PRO- 494	4.4	0	Hydrophobic	false
C9	CG	PRO- 494	3.38	0	Hydrophobic	false
C12	CG	PRO- 494	3.61	0	Hydrophobic	false
C14	CB	SER- 497	4.33	0	Hydrophobic	false
C9	CB	SER- 497	3.62	0	Hydrophobic	false
F1	CB	SER- 497	3.22	0	Hydrophobic	false
C5	CB	SER- 729	4.12	0	Hydrophobic	false
C3	CG1	VAL- 750	3.53	0	Hydrophobic	false
C19	CD2	LEU- 751	3.88	0	Hydrophobic	false
C3	CD2	LEU- 751	3.27	0	Hydrophobic	false
C2	CB	ASN- 754	4.32	0	Hydrophobic	false
C4	CB	ASN- 754	4.37	0	Hydrophobic	false
C19	CB	ASN- 754	4.4	0	Hydrophobic	false
O4	O	HOH- 1094	2.74	120.11	H-Bond (Protein Donor)	false