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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:

4iva

1.500 Å

X-ray

2013-01-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Tyrosine-protein kinase JAK2
ID:JAK2_HUMAN
AC:O60674
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:19.439
Number of residues:32
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.086405.000

% Hydrophobic% Polar
46.6753.33
According to VolSite

Ligand :
4iva_1 Structure
HET Code: 1J5
Formula: C17H19N5O
Molecular weight: 309.366 g/mol
DrugBank ID: -
Buried Surface Area:66.83 %
Polar Surface area: 90.52 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-14.9117-9.22683-11.2883


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
C1CD2LEU- 8554.390Hydrophobic
C25CBLEU- 8554.180Hydrophobic
C7CD1LEU- 8554.180Hydrophobic
C25CBVAL- 8633.670Hydrophobic
C24CG2VAL- 8633.650Hydrophobic
N16OGLU- 9302.95172.44H-Bond
(Ligand Donor)
N11NLEU- 9323.07174.09H-Bond
(Protein Donor)
O4NSER- 9363.34123.98H-Bond
(Protein Donor)
C7CD2LEU- 9833.450Hydrophobic
C13CD1LEU- 9833.60Hydrophobic
C20CD2LEU- 9833.910Hydrophobic
C22CBASP- 9944.160Hydrophobic
N27OHOH- 14383.18131.67H-Bond
(Protein Donor)
O4OHOH- 14912.52156.96H-Bond
(Ligand Donor)