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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:

3h9f

2.600 Å

X-ray

2009-04-30

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:30.232
Number of residues:34
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
1.057475.875

% Hydrophobic% Polar
58.8741.13
According to VolSite

Ligand :
3h9f_1 Structure
HET Code: 92M
Formula: C25H34N6O3
Molecular weight: 466.576 g/mol
DrugBank ID: -
Buried Surface Area:61.74 %
Polar Surface area: 94.06 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 2
Rings: 5
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
0.49597118.735347.8371


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
CBCCD1ILE- 5314.260Hydrophobic
CBACD1ILE- 5313.820Hydrophobic
CAFCG2ILE- 5313.60Hydrophobic
CAQCG2ILE- 5313.910Hydrophobic
CADCG2VAL- 5394.250Hydrophobic
CAGCG2VAL- 5394.210Hydrophobic
CACCD1ILE- 5864.270Hydrophobic
CBCSGCYS- 6044.330Hydrophobic
N1NGLY- 6053.1144.94H-Bond
(Protein Donor)
NANOGLY- 6053.19161.75H-Bond
(Ligand Donor)
CAXCG1ILE- 6074.160Hydrophobic
CAJCBASP- 6084.280Hydrophobic
CAXCBSER- 6113.470Hydrophobic
CAPCD1LEU- 6543.940Hydrophobic
CAJCD1ILE- 6634.280Hydrophobic
CACCD1ILE- 6633.780Hydrophobic
CAGSDMET- 6714.40Hydrophobic
CAYCBPRO- 6733.970Hydrophobic
CAICGPRO- 6734.060Hydrophobic