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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:

3c9t

2.600 Å

X-ray

2008-02-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Thiamine-monophosphate kinase
ID:THIL_AQUAE
AC:O67883
Organism:Aquifex aeolicus
Reign:Bacteria
TaxID:224324
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A15 %
B85 %


Ligand binding site composition:

B-Factor:48.496
Number of residues:33
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 4
Water Molecules: 0
Cofactors: ACP
Metals: MG MG MG

Cavity properties

LigandabilityVolume (Å3)
0.418502.875

% Hydrophobic% Polar
46.3153.69
According to VolSite

Ligand :
3c9t_2 Structure
HET Code: TPS
Formula: C12H16N4O4PS
Molecular weight: 343.319 g/mol
DrugBank ID: DB03416
Buried Surface Area:65.5 %
Polar Surface area: 166.15 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
37.345763.5615130.777


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
N4AOHIS- 503.22143.35H-Bond
(Ligand Donor)
O3NE2HIS- 502.74148.1H-Bond
(Protein Donor)
CM2CD2LEU- 523.720Hydrophobic
C5ACD2LEU- 1643.50Hydrophobic
CM4CGGLU- 2603.680Hydrophobic
C6CGGLU- 2603.990Hydrophobic
N4AOE1GLU- 2602.83151.32H-Bond
(Ligand Donor)
CM4CE3TRP- 3034.350Hydrophobic
C6CBTRP- 3034.010Hydrophobic
DuArDuArTRP- 3033.60Aromatic Face/Face
O1NE2HIS- 3053.14131.95H-Bond
(Protein Donor)
O1MG MG- 3102.740Metal Acceptor
O2MG MG- 3142.320Metal Acceptor