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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:

2j7t

2.000 Å

X-ray

2006-10-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Serine/threonine-protein kinase 10
ID:STK10_HUMAN
AC:O94804
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:40.092
Number of residues:39
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: CA

Cavity properties

LigandabilityVolume (Å3)
0.977934.875

% Hydrophobic% Polar
55.9644.04
According to VolSite

Ligand :
2j7t_1 Structure
HET Code: 274
Formula: C28H31ClN5O4S
Molecular weight: 569.095 g/mol
DrugBank ID: -
Buried Surface Area:57.93 %
Polar Surface area: 115.39 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-5.827136.71719.4606


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
C23CD2LEU- 424.190Hydrophobic
C7CG2VAL- 504.020Hydrophobic
C6CG1VAL- 504.240Hydrophobic
C12CBALA- 633.740Hydrophobic
C11CBALA- 633.830Hydrophobic
C6CBALA- 634.220Hydrophobic
CL1CDLYS- 654.410Hydrophobic
C4CBLYS- 653.910Hydrophobic
C5CGLYS- 654.140Hydrophobic
C2CDLYS- 654.030Hydrophobic
CL1CD2TYR- 784.170Hydrophobic
CL1CGGLU- 814.50Hydrophobic
C11CG1VAL- 943.930Hydrophobic
CL1CD1ILE- 1083.780Hydrophobic
C4CG2ILE- 1083.920Hydrophobic
C11CG2ILE- 1103.670Hydrophobic
C2CD1ILE- 1103.50Hydrophobic
C4CD1ILE- 1103.40Hydrophobic
N2OGLU- 1112.92154.06H-Bond
(Ligand Donor)
C23CE1PHE- 1124.060Hydrophobic
O3NCYS- 1132.89167.97H-Bond
(Protein Donor)
O4NALA- 1172.97170.27H-Bond
(Protein Donor)
C21CBALA- 1174.390Hydrophobic
C21CD2LEU- 1644.380Hydrophobic
C12CD1LEU- 1643.320Hydrophobic
C8CBALA- 1744.050Hydrophobic
O2NASP- 1752.78140.69H-Bond
(Protein Donor)
O2OHOH- 20072.82153.26H-Bond
(Protein Donor)