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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:

4kw5

2.610 Å

X-ray

2013-05-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Decaprenylphosphoryl-beta-D-ribose oxidase
ID:I6X8C4_MYCTU
AC:I6X8C4
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:53.475
Number of residues:32
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.948691.875

% Hydrophobic% Polar
46.3453.66
According to VolSite

Ligand :
4kw5_3 Structure
HET Code: 1W6
Formula: C16H12N3O4S2
Molecular weight: 374.414 g/mol
DrugBank ID: -
Buried Surface Area:57.37 %
Polar Surface area: 155.94 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-24.5587-24.38245.2664


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
O22OGSER- 2283.03164.17H-Bond
(Protein Donor)
C38CZ2TRP- 2303.350Hydrophobic
S27C6FAD- 5013.990Hydrophobic
C32C7MFAD- 5013.660Hydrophobic