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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:

4d0l

2.940 Å

X-ray

2014-04-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Phosphatidylinositol 4-kinase beta
ID:PI4KB_HUMAN
AC:Q9UBF8
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.1.67


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:57.141
Number of residues:30
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1151566.000

% Hydrophobic% Polar
43.3256.68
According to VolSite

Ligand :
4d0l_1 Structure
HET Code: 093
Formula: C14H16ClN3O4S2
Molecular weight: 389.878 g/mol
DrugBank ID: DB06836
Buried Surface Area:54.76 %
Polar Surface area: 141.54 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
7.69287335.3578.86433


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
SAPCD1ILE- 5473.650Hydrophobic
CAGCD1ILE- 5473.50Hydrophobic
CAECGTYR- 5833.630Hydrophobic
CLCD1ILE- 5953.980Hydrophobic
CADCG2ILE- 5954.280Hydrophobic
CAECG2ILE- 59540Hydrophobic
CABCD1ILE- 5953.810Hydrophobic
CAECBPRO- 5974.420Hydrophobic
SAPCBPRO- 5974.270Hydrophobic
NAKNVAL- 5982.88128.25H-Bond
(Protein Donor)
SAPCD2LEU- 6634.050Hydrophobic
CAECG2ILE- 6734.470Hydrophobic
CADCBILE- 6733.570Hydrophobic
CAHCD1ILE- 6733.920Hydrophobic