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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:

2vx0

2.100 Å

X-ray

2008-06-30

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:21.204
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.532489.375

% Hydrophobic% Polar
55.8644.14
According to VolSite

Ligand :
2vx0_1 Structure
HET Code: 7X7
Formula: C21H20ClN5O3
Molecular weight: 425.868 g/mol
DrugBank ID: DB07255
Buried Surface Area:57.2 %
Polar Surface area: 80.77 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 2
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
11.76446.9229311.7344


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
C13CD1ILE- 6213.650Hydrophobic
C13CG1VAL- 6294.30Hydrophobic
C5CBALA- 6453.790Hydrophobic
C6CBALA- 6454.40Hydrophobic
C9CBALA- 6453.340Hydrophobic
C5CGLYS- 6473.990Hydrophobic
C6CGLYS- 6474.030Hydrophobic
C3CDLYS- 6473.710Hydrophobic
C3CEMET- 6684.130Hydrophobic
C9CD1ILE- 6773.750Hydrophobic
C1CD1ILE- 6774.220Hydrophobic
C5CG2THR- 6933.760Hydrophobic
C4CG2THR- 6933.690Hydrophobic
N2NMET- 6962.94163.24H-Bond
(Protein Donor)
N3OMET- 6962.87159.78H-Bond
(Ligand Donor)
C9CD1LEU- 7473.630Hydrophobic
CL1CD1LEU- 7473.790Hydrophobic
CL1CBSER- 7573.940Hydrophobic