Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4gk3

1.900 Å

X-ray

2012-08-10

Interactomes:
Molecular Function:
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
A100 %


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

LigandabilityVolume (Å3)
1.237479.250

% Hydrophobic% Polar
51.4148.59
According to VolSite

Ligand :
4gk3_1 Structure
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

XYZ
20.1144-10.842523.0486


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C18CG2VAL- 6274.30Hydrophobic
C6CG2VAL- 6354.270Hydrophobic
C26CBALA- 6513.80Hydrophobic
C6CDLYS- 6534.210Hydrophobic
C13CDLYS- 6534.440Hydrophobic
C26CGLYS- 6533.40Hydrophobic
C13CGGLU- 6704.490Hydrophobic
C13CEMET- 6743.280Hydrophobic
C12CG2ILE- 6973.650Hydrophobic
C12CG2THR- 6993.280Hydrophobic
N4OMET- 7022.85127.7H-Bond
(Ligand Donor)
O3NMET- 7022.84151.09H-Bond
(Protein Donor)
C8CD1LEU- 7533.980Hydrophobic
C9CD2LEU- 7533.820Hydrophobic
C15CBSER- 7634.420Hydrophobic
C9CBSER- 7633.760Hydrophobic
C9CBASP- 7644.160Hydrophobic