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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:

3b6p

2.300 Å

X-ray

2007-10-29

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
C100 %


Ligand binding site composition:

B-Factor:28.547
Number of residues:28
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 2
Water Molecules: 4
Cofactors:
Metals: ZN NA

Cavity properties

LigandabilityVolume (Å3)
0.540465.750

% Hydrophobic% Polar
44.2055.80
According to VolSite

Ligand :
3b6p_3 Structure
HET Code: TMP
Formula: C10H13N2O8P
Molecular weight: 320.193 g/mol
DrugBank ID: -
Buried Surface Area:54.1 %
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
58.8011-3.89533-6.05586


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- 202.84163.16H-Bond
(Ligand Donor)
O3'NALA- 212.7170.88H-Bond
(Protein Donor)
C2'CBALA- 814.060Hydrophobic
C2'CD1ILE- 844.30Hydrophobic
C5MCD1ILE- 844.210Hydrophobic
C3'CG2THR- 854.010Hydrophobic
C5'CE2TYR- 1293.810Hydrophobic
C4'CZTYR- 1293.760Hydrophobic
C1'CZTYR- 1294.430Hydrophobic
O3PZN ZN- 8002.140Metal Acceptor