scPDB - 4h8i entry

Protein Data Bank Entry:

PDB ID : 4h8i

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-09-22

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 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:	34.928
Number of residues:	37
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.475	381.375

% Hydrophobic	% Polar
38.94	61.06
According to VolSite

Ligand :

HET Code:	11W
Formula:	C20H20N3O4
Molecular weight:	366.390 g/mol
DrugBank ID:	-
Buried Surface Area:	54.99 %
Polar Surface area:	132.62 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-4.72678	-26.6954	20.312

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
CAK	CG	LYS- 60	4.13	0	Hydrophobic	false
CB	CD2	TYR- 61	3.94	0	Hydrophobic	false
CAW	CE2	TYR- 61	3.4	0	Hydrophobic	false
N	O	PRO- 89	2.99	132.82	H-Bond (Ligand Donor)	false
OXT	N	ALA- 91	2.88	173.24	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 96	2.83	162.55	H-Bond (Protein Donor)	false
O	NH1	ARG- 96	3.22	128.47	H-Bond (Protein Donor)	false
O	NH2	ARG- 96	2.66	155.77	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 96	3.69	0	Ionic (Protein Cationic)	false
O	CZ	ARG- 96	3.35	0	Ionic (Protein Cationic)	false
CD1	CB	VAL- 138	4.04	0	Hydrophobic	false
CAW	CG1	VAL- 138	3.31	0	Hydrophobic	false
O	N	ALA- 142	2.84	155.54	H-Bond (Protein Donor)	false
OAE	N	THR- 143	2.77	165.73	H-Bond (Protein Donor)	false
OAC	OG1	THR- 143	2.77	171.38	H-Bond (Protein Donor)	false
CAP	CB	SER- 173	4.48	0	Hydrophobic	false
N	OE1	GLU- 191	2.85	157.11	H-Bond (Ligand Donor)	false
N	OE2	GLU- 191	3.26	137.55	H-Bond (Ligand Donor)	false
N	OE1	GLU- 191	2.85	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 191	3.26	0	Ionic (Ligand Cationic)	false
OAC	O	HOH- 448	3.44	129.27	H-Bond (Protein Donor)	false