scPDB - 2xyu entry

Protein Data Bank Entry:

PDB ID : 2xyu

Resolution :2.120 Å

Experimental Method : X-ray

Deposition Date : 2010-11-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ephrin type-A receptor 4
ID:	EPHA4_MOUSE
AC:	Q03137
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	2.7.10.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	25.425
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.073	502.875

% Hydrophobic	% Polar
50.34	49.66
According to VolSite

Ligand :

HET Code:	Q9G
Formula:	C17H17FN4
Molecular weight:	296.342 g/mol
DrugBank ID:	-
Buried Surface Area:	66.31 %
Polar Surface area:	67.59 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
4.04614	11.3342	19.5619

Binding mode :

What is Poseview ?

2D View
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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
C22	CG1	VAL- 635	4.05	0	Hydrophobic	false
C10	CG2	VAL- 635	3.87	0	Hydrophobic	false
C04	CG1	VAL- 635	4.3	0	Hydrophobic	false
C22	CB	ALA- 651	3.94	0	Hydrophobic	false
C03	CB	ALA- 651	3.81	0	Hydrophobic	false
C20	CD	LYS- 653	3.83	0	Hydrophobic	false
C22	CB	LYS- 653	3.63	0	Hydrophobic	false
F18	CE	MET- 674	3.68	0	Hydrophobic	false
F18	CG2	ILE- 683	4.16	0	Hydrophobic	false
C20	CG2	ILE- 697	4.17	0	Hydrophobic	false
N01	OG1	THR- 699	2.84	138.56	H-Bond (Protein Donor)	false
C22	CG2	THR- 699	4.39	0	Hydrophobic	false
C20	CG2	THR- 699	3.93	0	Hydrophobic	false
N12	O	GLU- 700	2.93	164.58	H-Bond (Ligand Donor)	false
N13	N	MET- 702	2.61	151.01	H-Bond (Protein Donor)	false
N15	O	MET- 702	3.16	148.6	H-Bond (Ligand Donor)	false
C03	CD1	LEU- 753	3.75	0	Hydrophobic	false
C05	CD1	LEU- 753	4.02	0	Hydrophobic	false
C16	CD1	LEU- 753	4.35	0	Hydrophobic	false
C04	CD2	LEU- 753	3.74	0	Hydrophobic	false
F18	CB	SER- 763	4.47	0	Hydrophobic	false