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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:

1kic

1.600 Å

X-ray

2001-12-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:IAG-nucleoside hydrolase
ID:Q9GPQ4_TRYVI
AC:Q9GPQ4
Organism:Trypanosoma vivax
Reign:Eukaryota
TaxID:5699
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:22.764
Number of residues:25
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: CA

Cavity properties

LigandabilityVolume (Å3)
0.616678.375

% Hydrophobic% Polar
47.2652.74
According to VolSite

Ligand :
1kic_1 Structure
HET Code: NOS
Formula: C10H12N4O5
Molecular weight: 268.226 g/mol
DrugBank ID: DB04335
Buried Surface Area:63.51 %
Polar Surface area: 133.75 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-0.1574213.1675830.8466


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
C4'SDMET- 1643.730Hydrophobic
O5'ND2ASN- 1732.98161.83H-Bond
(Protein Donor)
O5'OE1GLU- 1842.56174.28H-Bond
(Ligand Donor)
O3'ND2ASN- 1863.17134.67H-Bond
(Protein Donor)
C2'CE3TRP- 2603.60Hydrophobic
C3'CBTRP- 2603.990Hydrophobic
C5'CD2TRP- 2603.690Hydrophobic
O3'OD1ASP- 2612.69151.37H-Bond
(Ligand Donor)
O2'CA CA- 3282.580Metal Acceptor
O3'CA CA- 3282.410Metal Acceptor