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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:

4bi0

2.840 Å

X-ray

2013-04-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dual specificity protein kinase TTK
ID:TTK_HUMAN
AC:P33981
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.12.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:58.260
Number of residues:17
Including
Standard Amino Acids: 17
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.027924.750

% Hydrophobic% Polar
45.2654.74
According to VolSite

Ligand :
4bi0_1 Structure
HET Code: Z0W
Formula: C10H7N3
Molecular weight: 169.183 g/mol
DrugBank ID: -
Buried Surface Area:57.33 %
Polar Surface area: 41.57 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
-0.40330843.10717.5889


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
C5CG2ILE- 5313.330Hydrophobic
C12CG2ILE- 5314.070Hydrophobic
C11CG1VAL- 5394.070Hydrophobic
C8CBALA- 5513.630Hydrophobic
C9CD1ILE- 5863.270Hydrophobic
C10SDMET- 6024.160Hydrophobic
N1NGLY- 6053.2141.21H-Bond
(Protein Donor)
C5CD1LEU- 6543.550Hydrophobic
C8CD2LEU- 6543.920Hydrophobic
C7CD1LEU- 6543.970Hydrophobic
C11CG2ILE- 6634.190Hydrophobic