scPDB - 2cmo entry

Protein Data Bank Entry:

PDB ID : 2cmo

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2006-05-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate receptor 2
ID:	GRIA2_RAT
AC:	P19491
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:	21.155
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.405	627.750

% Hydrophobic	% Polar
39.25	60.75
According to VolSite

Ligand :

HET Code:	M1L
Formula:	C24H30N4O7S
Molecular weight:	518.583 g/mol
DrugBank ID:	-
Buried Surface Area:	53.26 %
Polar Surface area:	159.19 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
5.37469	28.1819	23.0422

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
C1	CG	GLU- 13	4.14	0	Hydrophobic	false
C3	CB	TYR- 61	4.42	0	Hydrophobic	false
O7	N	TYR- 61	3.09	155.69	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 61	3.76	0	Aromatic Face/Face	false
O6	N	GLY- 62	3.29	135.63	H-Bond (Protein Donor)	false
N2	O	PRO- 89	3.03	147.6	H-Bond (Ligand Donor)	false
O1	N	THR- 91	3.04	168.15	H-Bond (Protein Donor)	false
O1	OG1	THR- 91	3.28	134.58	H-Bond (Protein Donor)	false
O1	NH2	ARG- 96	3.3	125.44	H-Bond (Protein Donor)	false
O1	NH1	ARG- 96	2.73	145.38	H-Bond (Protein Donor)	false
N3	NH2	ARG- 96	3	156.29	H-Bond (Protein Donor)	false
O6	NH2	ARG- 96	3.12	138.76	H-Bond (Protein Donor)	false
C21	CD2	LEU- 138	3.61	0	Hydrophobic	false
C14	CD2	LEU- 138	3.63	0	Hydrophobic	false
O5	N	SER- 142	3.25	120.41	H-Bond (Protein Donor)	false
O3	OG1	THR- 174	3.38	173.59	H-Bond (Protein Donor)	false
O3	N	THR- 174	2.89	144.83	H-Bond (Protein Donor)	false
N1	OE2	GLU- 193	2.55	169.92	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 193	3.45	125.51	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 193	2.55	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 193	3.45	0	Ionic (Ligand Cationic)	false
C1	SD	MET- 196	3.99	0	Hydrophobic	false