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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:

1t6y

2.800 Å

X-ray

2004-05-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Riboflavin biosynthesis protein
ID:Q9WZW1_THEMA
AC:Q9WZW1
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:91.881
Number of residues:20
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: FMN
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.451286.875

% Hydrophobic% Polar
54.1245.88
According to VolSite

Ligand :
1t6y_3 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:52.95 %
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
-10.4293-8.8035925.4566


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
C3'CG1VAL- 4664.490Hydrophobic
C5'CBPRO- 4794.230Hydrophobic
O3ANTHR- 4803.07167.15H-Bond
(Protein Donor)
C2'CBALA- 4814.490Hydrophobic
N6OILE- 5343.19157.86H-Bond
(Ligand Donor)
N1NILE- 5343.26136.56H-Bond
(Protein Donor)
N6OPHE- 5373.05157.87H-Bond
(Ligand Donor)
O3'OD2ASP- 5403.26138.92H-Bond
(Ligand Donor)
O2'NLEU- 5413.02128.07H-Bond
(Protein Donor)