scPDB - 5ewj entry

Protein Data Bank Entry:

PDB ID : 5ewj

Resolution :2.770 Å

Experimental Method : X-ray

Deposition Date : 2015-11-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.030	7.030	7.030	0.000	7.030	1

List of CHEMBLId :

CHEMBL49623

Binding Site :

Uniprot Annotation

Name:	NMDA glutamate receptor subunit	Glutamate receptor ionotropic, NMDA 2B
ID:	Q91977_XENLA	NMDE2_HUMAN
AC:	Q91977	Q13224
Organism:	Xenopus laevis	Homo sapiens
Reign:	Eukaryota
TaxID:	8355	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	47 %
B	53 %

Ligand binding site composition:

B-Factor:	47.626
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.223	1353.375

% Hydrophobic	% Polar
44.39	55.61
According to VolSite

Ligand :

HET Code:	QEL
Formula:	C21H28NO2
Molecular weight:	326.453 g/mol
DrugBank ID:	-
Buried Surface Area:	70.2 %
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:	5

Mass center Coordinates

X	Y	Z
85.6098	6.40154	-31.9116

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
C01	CB	PRO- 78	3.88	0	Hydrophobic	false
C02	CG	PRO- 78	3.9	0	Hydrophobic	false
C12	CB	ALA- 107	3.74	0	Hydrophobic	false
C9	CB	TYR- 109	4.21	0	Hydrophobic	false
C1	CB	TYR- 109	3.57	0	Hydrophobic	false
C5	CB	TYR- 109	3.69	0	Hydrophobic	false
C01	CB	THR- 110	4.37	0	Hydrophobic	false
N1	OE1	GLN- 110	2.89	170.47	H-Bond (Ligand Donor)	false
C5	CB	GLN- 110	4.42	0	Hydrophobic	false
C7	CB	GLN- 110	4.1	0	Hydrophobic	false
C9	CB	GLN- 110	4.29	0	Hydrophobic	false
C4	CG1	ILE- 111	3.71	0	Hydrophobic	false
C7	CD2	PHE- 113	3.99	0	Hydrophobic	false
C8	CB	PHE- 113	4.14	0	Hydrophobic	false
C02	CB	PHE- 113	4.42	0	Hydrophobic	false
C12	CD2	PHE- 113	3.99	0	Hydrophobic	false
C6	CB	PHE- 114	3.81	0	Hydrophobic	false
O1	O	SER- 132	2.83	153.69	H-Bond (Ligand Donor)	false
C3	CD1	LEU- 135	3.83	0	Hydrophobic	false
C24	CB	LEU- 135	3.45	0	Hydrophobic	false
C19	CD2	LEU- 135	4.06	0	Hydrophobic	false
C18	CB	PHE- 176	4.08	0	Hydrophobic	false
C19	CG	PRO- 177	4.35	0	Hydrophobic	false
C2	CG2	THR- 233	4.4	0	Hydrophobic	false
O2	OE2	GLU- 236	2.55	161.9	H-Bond (Ligand Donor)	false
O2	O	HOH- 610	2.78	179.95	H-Bond (Protein Donor)	false