scPDB - 4dld entry

Protein Data Bank Entry:

PDB ID : 4dld

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-02-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.520	5.520	5.520	0.000	5.520	1

List of CHEMBLId :

CHEMBL1835336

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:	18.842
Number of residues:	33
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.824	772.875

% Hydrophobic	% Polar
39.30	60.70
According to VolSite

Ligand :

HET Code:	TZG
Formula:	C12H12ClN2O6
Molecular weight:	315.686 g/mol
DrugBank ID:	-
Buried Surface Area:	74.27 %
Polar Surface area:	153.72 Å2

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

Mass center Coordinates

X	Y	Z
-0.38419	35.2304	102.916

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
CL1	CG	GLU- 13	3.75	0	Hydrophobic	false
CL1	CE2	TYR- 16	3.34	0	Hydrophobic	false
C7	CE2	TYR- 61	3.33	0	Hydrophobic	false
N2	O	PRO- 88	3.07	162.7	H-Bond (Ligand Donor)	false
CL1	CB	PRO- 88	3.62	0	Hydrophobic	false
C4	CG	PRO- 88	3.99	0	Hydrophobic	false
O5	N	THR- 90	2.72	173.48	H-Bond (Protein Donor)	false
N2	OG1	THR- 90	2.77	158.74	H-Bond (Ligand Donor)	false
O4	CZ	ARG- 95	3.6	0	Ionic (Protein Cationic)	false
O5	CZ	ARG- 95	3.67	0	Ionic (Protein Cationic)	false
O4	NH2	ARG- 95	2.84	171.88	H-Bond (Protein Donor)	false
O4	NH1	ARG- 95	3.49	131.68	H-Bond (Protein Donor)	false
O5	NH1	ARG- 95	2.82	158.35	H-Bond (Protein Donor)	false
C10	CB	VAL- 137	3.77	0	Hydrophobic	false
O7	N	THR- 142	2.93	140.77	H-Bond (Protein Donor)	false
N1	OG	SER- 173	3.38	141.77	H-Bond (Protein Donor)	false
O1	OG	SER- 173	2.67	146.81	H-Bond (Protein Donor)	false
N2	OE2	GLU- 190	3.12	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 190	2.84	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 190	2.84	155.96	H-Bond (Ligand Donor)	false
CL1	CZ	TYR- 216	4.42	0	Hydrophobic	false
O6	O	HOH- 491	3.13	179.99	H-Bond (Protein Donor)	false