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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:

2o4g

2.350 Å

X-ray

2006-12-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Three-prime repair exonuclease 1
ID:TREX1_MOUSE
AC:Q91XB0
Organism:Mus musculus
Reign:Eukaryota
TaxID:10090
EC Number:3.1.11.2


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:23.772
Number of residues:28
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 2
Water Molecules: 3
Cofactors:
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
0.238459.000

% Hydrophobic% Polar
47.0652.94
According to VolSite

Ligand :
2o4g_2 Structure
HET Code: TMP
Formula: C10H13N2O8P
Molecular weight: 320.193 g/mol
DrugBank ID: -
Buried Surface Area:57.61 %
Polar Surface area: 161.1 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 2
Rings: 2
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
2.92167-4.1376728.8869


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
O3'OE1GLU- 202.67163.6H-Bond
(Ligand Donor)
C4'CBALA- 214.420Hydrophobic
O3'NALA- 212.81152.47H-Bond
(Protein Donor)
C1'CD2LEU- 243.650Hydrophobic
C2'CBALA- 814.110Hydrophobic
C2'CD1ILE- 844.350Hydrophobic
C3'CG2THR- 853.980Hydrophobic
C5'CE2TYR- 1293.730Hydrophobic
C4'CZTYR- 1293.820Hydrophobic
O3PMG MG- 8002.210Metal Acceptor
O3PMG MG- 8012.370Metal Acceptor