scPDB - 4bdr entry

Protein Data Bank Entry:

PDB ID : 4bdr

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2012-10-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	4.910	4.910	4.910	0.000	4.920	3

List of CHEMBLId :

CHEMBL279561

Binding Site :

Uniprot Annotation

Name:	Glutamate receptor ionotropic, kainate 2
ID:	GRIK2_RAT
AC:	P42260
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:	23.657
Number of residues:	37
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.544	378.000

% Hydrophobic	% Polar
51.79	48.21
According to VolSite

Ligand :

HET Code:	KAI
Formula:	C10H14NO4
Molecular weight:	212.222 g/mol
DrugBank ID:	-
Buried Surface Area:	73.11 %
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
-27.9502	34.7885	5.72047

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
CD1	CG	GLU- 440	4.13	0	Hydrophobic	false
CD1	CZ	TYR- 488	3.36	0	Hydrophobic	false
CG	CZ	TYR- 488	3.6	0	Hydrophobic	false
CD2	CE1	TYR- 488	3.45	0	Hydrophobic	false
N	O	PRO- 516	2.88	129.31	H-Bond (Ligand Donor)	false
O	N	ALA- 518	2.97	175.48	H-Bond (Protein Donor)	false
O	NH1	ARG- 523	2.88	161.97	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 523	2.82	155.8	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 523	3.4	129.76	H-Bond (Protein Donor)	false
O	CZ	ARG- 523	3.65	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 523	3.53	0	Ionic (Protein Cationic)	false
CD2	CG1	VAL- 685	3.82	0	Hydrophobic	false
OXT	N	ALA- 689	3	149.9	H-Bond (Protein Donor)	false
OD1	OG1	THR- 690	2.61	177.53	H-Bond (Protein Donor)	false
OD2	N	THR- 690	3.03	168.54	H-Bond (Protein Donor)	false
OD2	OG1	THR- 690	3.29	122.78	H-Bond (Protein Donor)	false
N	OE2	GLU- 738	3.28	127.38	H-Bond (Ligand Donor)	false
N	OE1	GLU- 738	2.87	156.88	H-Bond (Ligand Donor)	false
N	OE2	GLU- 738	3.28	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 738	2.87	0	Ionic (Ligand Cationic)	false
CB1	CG	GLU- 738	4.44	0	Hydrophobic	false
OD1	O	HOH- 2132	2.87	147.74	H-Bond (Protein Donor)	false
OD2	O	HOH- 2133	2.75	146.79	H-Bond (Protein Donor)	false
OD1	O	HOH- 2180	2.7	144.93	H-Bond (Protein Donor)	false