scPDB - 2y6o entry

Protein Data Bank Entry:

PDB ID : 2y6o

Resolution :1.540 Å

Experimental Method : X-ray

Deposition Date : 2011-01-25

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:	18.725
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.293	496.125

% Hydrophobic	% Polar
53.74	46.26
According to VolSite

Ligand :

HET Code:	1N1
Formula:	C22H27ClN7O2S
Molecular weight:	489.013 g/mol
DrugBank ID:	DB01254
Buried Surface Area:	56.44 %
Polar Surface area:	135.94 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
25.0562	59.3747	29.3439

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
C12	CD1	ILE- 627	4.28	0	Hydrophobic	false
C15	CG1	ILE- 627	4.06	0	Hydrophobic	false
S	CG1	VAL- 635	4.26	0	Hydrophobic	false
C10	CB	ALA- 651	3.77	0	Hydrophobic	false
S	CB	ALA- 651	4.24	0	Hydrophobic	false
C7	CD	LYS- 653	4.22	0	Hydrophobic	false
C8	CB	LYS- 653	3.57	0	Hydrophobic	false
C7	CE	MET- 674	3.67	0	Hydrophobic	false
CL	CG1	ILE- 683	4.15	0	Hydrophobic	false
C8	CG2	ILE- 697	3.51	0	Hydrophobic	false
N2	OG1	THR- 699	2.9	151	H-Bond (Ligand Donor)	false
C5	CG2	THR- 699	3.97	0	Hydrophobic	false
C9	CG2	THR- 699	3.36	0	Hydrophobic	false
N	O	MET- 702	2.84	154.35	H-Bond (Ligand Donor)	false
N1	N	MET- 702	3.01	170.34	H-Bond (Protein Donor)	false
S	CD1	LEU- 753	4.22	0	Hydrophobic	false
CL	CD1	LEU- 753	4.03	0	Hydrophobic	false
CL	CB	SER- 763	3.78	0	Hydrophobic	false