scPDB - 3qem entry

Protein Data Bank Entry:

PDB ID : 3qem

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2011-01-20

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, NMDA 2B	NMDA glutamate receptor subunit
ID:	NMDE2_RAT	Q91977_XENLA
AC:	Q00960	Q91977
Organism:	Rattus norvegicus	Xenopus laevis
Reign:	Eukaryota
TaxID:	10116	8355
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	46 %
B	54 %

Ligand binding site composition:

B-Factor:	47.316
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.317	1302.750

% Hydrophobic	% Polar
48.45	51.55
According to VolSite

Ligand :

HET Code:	QEM
Formula:	C22H30NO2
Molecular weight:	340.479 g/mol
DrugBank ID:	-
Buried Surface Area:	69.2 %
Polar Surface area:	44.9 Å2

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

Mass center Coordinates

X	Y	Z
85.9641	6.6764	-32.2155

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
C03	CG	PRO- 78	4.05	0	Hydrophobic	false
C04	CB	PRO- 78	3.96	0	Hydrophobic	false
C09	CB	ALA- 107	3.79	0	Hydrophobic	false
C12	CB	TYR- 109	3.65	0	Hydrophobic	false
C03	CB	TYR- 109	3.75	0	Hydrophobic	false
C04	CB	THR- 110	4.3	0	Hydrophobic	false
N	OE1	GLN- 110	2.97	175.33	H-Bond (Ligand Donor)	false
C07	CB	GLN- 110	3.72	0	Hydrophobic	false
C07	CG1	ILE- 111	3.93	0	Hydrophobic	false
C02	CG1	ILE- 111	3.76	0	Hydrophobic	false
C03	CB	PHE- 113	4.35	0	Hydrophobic	false
C09	CD1	PHE- 113	4.03	0	Hydrophobic	false
C06	CB	PHE- 114	3.71	0	Hydrophobic	false
C15	CB	LEU- 135	3.81	0	Hydrophobic	false
C18	CD1	LEU- 135	3.23	0	Hydrophobic	false
C19	CB	TYR- 175	4.1	0	Hydrophobic	false
C17	CE1	PHE- 176	4.39	0	Hydrophobic	false
C20	CB	PHE- 176	4.3	0	Hydrophobic	false
C17	CG	PRO- 177	3.83	0	Hydrophobic	false
O	OE2	GLU- 236	2.72	156.32	H-Bond (Ligand Donor)	false
O	OE1	GLU- 236	3.36	126.19	H-Bond (Ligand Donor)	false