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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:

3nuy

2.100 Å

X-ray

2010-07-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-phosphoinositide-dependent protein kinase 1
ID:PDPK1_HUMAN
AC:O15530
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:34.294
Number of residues:18
Including
Standard Amino Acids: 18
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.683455.625

% Hydrophobic% Polar
47.4152.59
According to VolSite

Ligand :
3nuy_1 Structure
HET Code: JPZ
Formula: C8H6N2O
Molecular weight: 146.146 g/mol
DrugBank ID: -
Buried Surface Area:63.1 %
Polar Surface area: 41.46 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
-41.351815.097312.133


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
C9CBLEU- 883.990Hydrophobic
C8CG2VAL- 963.860Hydrophobic
C11CG1VAL- 964.270Hydrophobic
C11CBALA- 1094.240Hydrophobic
N3OSER- 1602.69143.68H-Bond
(Ligand Donor)
O1NALA- 1623.08178.09H-Bond
(Protein Donor)
C7CD1LEU- 2124.390Hydrophobic
C11CD1LEU- 2123.520Hydrophobic
C7CG2THR- 2224.390Hydrophobic
N5OG1THR- 2223.19164.64H-Bond
(Protein Donor)