scPDB - 2pbw entry

Protein Data Bank Entry:

PDB ID : 2pbw

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-03-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.960	8.960	8.960	0.000	8.970	2

List of CHEMBLId :

CHEMBL482097

Binding Site :

Uniprot Annotation

Name:	Glutamate receptor ionotropic, kainate 1
ID:	GRIK1_RAT
AC:	P22756
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:	10.665
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.375	729.000

% Hydrophobic	% Polar
37.50	62.50
According to VolSite

Ligand :

HET Code:	DOQ
Formula:	C15H19NO6
Molecular weight:	309.314 g/mol
DrugBank ID:	DB02852
Buried Surface Area:	62.34 %
Polar Surface area:	137 Å2

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

Mass center Coordinates

X	Y	Z
-3.99786	-34.4645	78.3616

Binding mode :

What is Poseview ?

2D View
3D View

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
OAD	N	TYR- 61	2.79	149.86	H-Bond (Protein Donor)	false
CAS	CD1	TYR- 61	4.27	0	Hydrophobic	false
CAA	CZ	TYR- 61	4.35	0	Hydrophobic	false
CAT	CZ	TYR- 61	3.82	0	Hydrophobic	false
N	O	PRO- 88	3.02	129.11	H-Bond (Ligand Donor)	false
OXT	N	THR- 90	3.33	158.65	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 95	2.7	167.25	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 95	3.32	130.53	H-Bond (Protein Donor)	false
O	NH2	ARG- 95	3.11	136.19	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 95	3.44	0	Ionic (Protein Cationic)	false
O	CZ	ARG- 95	3.71	0	Ionic (Protein Cationic)	false
CAB	CG1	VAL- 137	4.21	0	Hydrophobic	false
CAB	CB	ASP- 139	3.76	0	Hydrophobic	false
O	OG	SER- 141	2.65	153.56	H-Bond (Protein Donor)	false
O	N	SER- 141	2.75	143.98	H-Bond (Protein Donor)	false
OE2	N	THR- 142	2.93	175.86	H-Bond (Protein Donor)	false
OE1	OG1	THR- 142	2.61	166.62	H-Bond (Protein Donor)	false
N	OE2	GLU- 190	3.72	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 190	2.98	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 190	2.98	149.64	H-Bond (Ligand Donor)	false
CG	CG	GLU- 190	4.42	0	Hydrophobic	false
OE2	O	HOH- 426	2.6	148.04	H-Bond (Protein Donor)	false
OE1	O	HOH- 464	3.2	130.88	H-Bond (Protein Donor)	false