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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:

3ihk

3.000 Å

X-ray

2009-07-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:Q8DVV9_STRMU
AC:Q8DVV9
Organism:Streptococcus mutans serotype c
Reign:Bacteria
TaxID:210007
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B49 %
C51 %


Ligand binding site composition:

B-Factor:46.721
Number of residues:37
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
0.9981353.375

% Hydrophobic% Polar
28.4371.57
According to VolSite

Ligand :
3ihk_3 Structure
HET Code: TPP
Formula: C12H16N4O7P2S
Molecular weight: 422.291 g/mol
DrugBank ID: -
Buried Surface Area:64.36 %
Polar Surface area: 225.32 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 8

Mass center Coordinates

XYZ
12.319952.108733.4967


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
C6CGLYS- 714.230Hydrophobic
N4'OD1ASN- 723.16145.47H-Bond
(Ligand Donor)
O2ANASP- 753.23171.61H-Bond
(Protein Donor)
O1BCZARG- 1013.620Ionic
(Protein Cationic)
O1BNH2ARG- 1012.67127.28H-Bond
(Protein Donor)
O1ANE2HIS- 1042.64123.65H-Bond
(Protein Donor)
O1BNE2HIS- 1042.64127.98H-Bond
(Protein Donor)
CM2CBTYR- 1694.390Hydrophobic
C7'CD2TYR- 1693.390Hydrophobic
CM4CZTYR- 1693.660Hydrophobic
CM2CBLEU- 1713.740Hydrophobic
CM2CZPHE- 1774.180Hydrophobic
CM2CBTYR- 1824.360Hydrophobic
C7'CBSER- 1844.490Hydrophobic
CM4CBSER- 1844.080Hydrophobic
C7CBSER- 1844.110Hydrophobic
O1BOGSER- 1843.11149.19H-Bond
(Protein Donor)