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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:

3go6

1.980 Å

X-ray

2009-03-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Ribokinase
ID:P71913_MYCTU
AC:P71913
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:27.601
Number of residues:36
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.982253.125

% Hydrophobic% Polar
57.3342.67
According to VolSite

Ligand :
3go6_1 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:64.69 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-8.06111-1.5221931.7878


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
C5'CBTHR- 2104.030Hydrophobic
C3'CBTHR- 2104.340Hydrophobic
O3'OGLY- 2152.63153.47H-Bond
(Ligand Donor)
C2'CBALA- 2294.370Hydrophobic
O1BOG1THR- 2373.4158.76H-Bond
(Protein Donor)
O3BNGLY- 2412.87160.56H-Bond
(Protein Donor)
C4'CD1PHE- 2444.140Hydrophobic
O2'OCYS- 2702.89126.96H-Bond
(Ligand Donor)
O5'OHOH- 4623.46130.46H-Bond
(Protein Donor)