scPDB - 2ojt entry

Protein Data Bank Entry:

PDB ID : 2ojt

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2007-01-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
B	100 %

Ligand binding site composition:

B-Factor:	35.881
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.173	1107.000

% Hydrophobic	% Polar
40.85	59.15
According to VolSite

Ligand :

HET Code:	UBA
Formula:	C14H14N3O6S
Molecular weight:	352.342 g/mol
DrugBank ID:	-
Buried Surface Area:	57.83 %
Polar Surface area:	176.76 Å2

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

Mass center Coordinates

X	Y	Z
-53.4044	-4.73738	16.5395

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
C6	CG	GLU- 13	4.02	0	Hydrophobic	false
C6	CE1	TYR- 16	3.83	0	Hydrophobic	false
CB	CE1	TYR- 61	3.57	0	Hydrophobic	false
N	O	PRO- 88	2.94	162.1	H-Bond (Ligand Donor)	false
C6	CB	PRO- 88	3.86	0	Hydrophobic	false
OXT	N	THR- 90	2.88	169.83	H-Bond (Protein Donor)	false
N	OG1	THR- 90	3.01	171.86	H-Bond (Ligand Donor)	false
OXT	CZ	ARG- 95	3.6	0	Ionic (Protein Cationic)	false
O	CZ	ARG- 95	3.63	0	Ionic (Protein Cationic)	false
OXT	NH1	ARG- 95	2.82	158.74	H-Bond (Protein Donor)	false
O	NH2	ARG- 95	2.84	168.99	H-Bond (Protein Donor)	false
S20	CB	VAL- 137	3.59	0	Hydrophobic	false
O2	OG1	THR- 142	2.69	160.34	H-Bond (Protein Donor)	false
O1	OG1	THR- 142	3.06	133.57	H-Bond (Protein Donor)	false
O1	N	THR- 142	2.77	158.52	H-Bond (Protein Donor)	false
C17	CG	GLU- 190	3.88	0	Hydrophobic	false