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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:

5a2y

2.750 Å

X-ray

2015-05-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Mitochondrial poly(A) polymerase
ID:F1NBW0_CHICK
AC:F1NBW0
Organism:Gallus gallus
Reign:Eukaryota
TaxID:9031
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:70.089
Number of residues:33
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.8881107.000

% Hydrophobic% Polar
38.7261.28
According to VolSite

Ligand :
5a2y_2 Structure
HET Code: UTP
Formula: C9H11N2O15P3
Molecular weight: 480.109 g/mol
DrugBank ID: DB04005
Buried Surface Area:40.42 %
Polar Surface area: 299.67 Å2
Number of
H-Bond Acceptors: 15
H-Bond Donors: 3
Rings: 2
Aromatic rings: 0
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-24.06891.932970.0602759


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
C4'CE2PHE- 2243.770Hydrophobic
O2GOGSER- 2262.56138.21H-Bond
(Protein Donor)
C1'CBALA- 3274.220Hydrophobic
C2'CBCYS- 3304.40Hydrophobic
O3GND2ASN- 3713.39137.26H-Bond
(Protein Donor)
C2'CE1PHE- 3724.020Hydrophobic
C3'CD1PHE- 3724.420Hydrophobic
O1BMG MG- 15292.40Metal Acceptor