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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:

5f8e

2.900 Å

X-ray

2015-12-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Possible transcriptional regulatory protein
ID:O53532_MYCTU
AC:O53532
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:56.999
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.5721933.875

% Hydrophobic% Polar
56.0243.98
According to VolSite

Ligand :
5f8e_1 Structure
HET Code: SAH
Formula: C14H20N6O5S
Molecular weight: 384.411 g/mol
DrugBank ID: DB01752
Buried Surface Area:56.58 %
Polar Surface area: 212.38 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
31.6739-37.592518.3751


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
SDCEMET- 1424.40Hydrophobic
OOGSER- 1463176.69H-Bond
(Protein Donor)
NOGLY- 1792.99150.56H-Bond
(Ligand Donor)
O3'OD2ASP- 2022.74174.7H-Bond
(Ligand Donor)
DuArDuArPHE- 2033.70Aromatic Face/Face
C2'CE1PHE- 2033.780Hydrophobic
N6OD1ASP- 2293.09151.34H-Bond
(Ligand Donor)
N1NLEU- 2302.8158.07H-Bond
(Protein Donor)
CBCBALA- 2474.40Hydrophobic
SDCBALA- 2474.270Hydrophobic
N7NE2GLN- 2513.25132.12H-Bond
(Protein Donor)