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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

2x9f

1.750 Å

X-ray

2010-03-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Ephrin type-B receptor 4
ID:EPHB4_HUMAN
AC:P54760
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:19.513
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.045786.375

% Hydrophobic% Polar
45.0654.94
According to VolSite

Ligand :
2x9f_1 Structure
HET Code: X9F
Formula: C18H16N6O2S
Molecular weight: 380.424 g/mol
DrugBank ID: -
Buried Surface Area:60.79 %
Polar Surface area: 121.04 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 4
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
11.94056.4099311.7861


Binding mode :
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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
C3CBILE- 6213.850Hydrophobic
C6CD1ILE- 6213.710Hydrophobic
C11CG1VAL- 6294.420Hydrophobic
C9CBALA- 6453.20Hydrophobic
C12CBALA- 6453.950Hydrophobic
C13CGLYS- 6473.610Hydrophobic
C14CDLYS- 6473.630Hydrophobic
N4OE2GLU- 6642.67162.48H-Bond
(Ligand Donor)
N4OE1GLU- 6643.44130.93H-Bond
(Ligand Donor)
C14CEMET- 6684.280Hydrophobic
C9CD1ILE- 6774.330Hydrophobic
C15CD1ILE- 6773.90Hydrophobic
C14CG2ILE- 6914.140Hydrophobic
C14CG2THR- 6933.580Hydrophobic
C1CZPHE- 6953.410Hydrophobic
N2NMET- 6962.97161.47H-Bond
(Protein Donor)
N1OMET- 6962.83165.1H-Bond
(Ligand Donor)
C9CD1LEU- 7473.490Hydrophobic
N5NASP- 7583.05148.77H-Bond
(Protein Donor)