scPDB - 4gk3 entry

Protein Data Bank Entry:

PDB ID : 4gk3

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-08-10

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 3
ID:	EPHA3_HUMAN
AC:	P29320
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.10.1

Chains:

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

Ligand binding site composition:

B-Factor:	21.983
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.237	479.250

% Hydrophobic	% Polar
51.41	48.59
According to VolSite

Ligand :

HET Code:	L87
Formula:	C19H21N5O2
Molecular weight:	351.402 g/mol
DrugBank ID:	-
Buried Surface Area:	64.97 %
Polar Surface area:	71.64 Å2

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

Mass center Coordinates

X	Y	Z
20.1144	-10.8425	23.0486

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
C18	CG2	VAL- 627	4.3	0	Hydrophobic	false
C6	CG2	VAL- 635	4.27	0	Hydrophobic	false
C26	CB	ALA- 651	3.8	0	Hydrophobic	false
C6	CD	LYS- 653	4.21	0	Hydrophobic	false
C13	CD	LYS- 653	4.44	0	Hydrophobic	false
C26	CG	LYS- 653	3.4	0	Hydrophobic	false
C13	CG	GLU- 670	4.49	0	Hydrophobic	false
C13	CE	MET- 674	3.28	0	Hydrophobic	false
C12	CG2	ILE- 697	3.65	0	Hydrophobic	false
C12	CG2	THR- 699	3.28	0	Hydrophobic	false
N4	O	MET- 702	2.85	127.7	H-Bond (Ligand Donor)	false
O3	N	MET- 702	2.84	151.09	H-Bond (Protein Donor)	false
C8	CD1	LEU- 753	3.98	0	Hydrophobic	false
C9	CD2	LEU- 753	3.82	0	Hydrophobic	false
C15	CB	SER- 763	4.42	0	Hydrophobic	false
C9	CB	SER- 763	3.76	0	Hydrophobic	false
C9	CB	ASP- 764	4.16	0	Hydrophobic	false