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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:

3rvg

2.500 Å

X-ray

2011-05-06

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:35.256
Number of residues:31
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.083435.375

% Hydrophobic% Polar
54.2645.74
According to VolSite

Ligand :
3rvg_1 Structure
HET Code: 17P
Formula: C22H24N6O
Molecular weight: 388.466 g/mol
DrugBank ID: -
Buried Surface Area:49.93 %
Polar Surface area: 101.62 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 5
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-24.824-35.47186.19279


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
C4CD1LEU- 8554.120Hydrophobic
C8CBLEU- 8553.920Hydrophobic
C9CD2LEU- 8553.990Hydrophobic
C15CG2VAL- 8634.30Hydrophobic
C4CBALA- 8803.880Hydrophobic
N20OGLU- 9302.79157.42H-Bond
(Ligand Donor)
C11CE1TYR- 9313.80Hydrophobic
NOLEU- 9322.88122.85H-Bond
(Ligand Donor)
ONLEU- 9322.75150.5H-Bond
(Protein Donor)
C4CD1LEU- 9833.750Hydrophobic
C19CD2LEU- 9834.320Hydrophobic
C18CBASP- 9944.50Hydrophobic