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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:

5kbw

2.610 Å

X-ray

2016-06-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Riboflavin transporter RibU
ID:RIBU_THEMA
AC:Q9X1G6
Organism:Thermotoga maritima
Reign:Bacteria
TaxID:243274
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:57.746
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.526388.125

% Hydrophobic% Polar
47.8352.17
According to VolSite

Ligand :
5kbw_1 Structure
HET Code: RBF
Formula: C17H20N4O6
Molecular weight: 376.364 g/mol
DrugBank ID: DB00140
Buried Surface Area:72.66 %
Polar Surface area: 155.04 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 5
Rings: 3
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-25.72750.070185283.1169


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
O4'OE1GLU- 243.31150.68H-Bond
(Ligand Donor)
C8MCBPHE- 334.480Hydrophobic
C7CD1PHE- 333.410Hydrophobic
C6CD2LEU- 344.230Hydrophobic
C9ACD2LEU- 3440Hydrophobic
O2'NLYS- 352.66159.34H-Bond
(Protein Donor)
O5'NZLYS- 353.36144.48H-Bond
(Protein Donor)
C4'CGLYS- 353.890Hydrophobic
C8MCG1VAL- 754.210Hydrophobic
C6CEMET- 794.370Hydrophobic
C9ACBMET- 794.070Hydrophobic
C1'CBASN- 804.310Hydrophobic
O4ND2ASN- 1232.79157.13H-Bond
(Protein Donor)
C7MCG2ILE- 1263.960Hydrophobic
C6CG2VAL- 1274.370Hydrophobic
C7MCG2VAL- 1273.720Hydrophobic
C7MCD2TYR- 1304.10Hydrophobic
C8MCZTYR- 1303.860Hydrophobic
N3OD1ASN- 1492.71168.85H-Bond
(Ligand Donor)
O4ND2ASN- 1492.9172.79H-Bond
(Protein Donor)
O2NZLYS- 1522.6151.28H-Bond
(Protein Donor)