Ligand profile

DUT

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_5009 — deoxycytidine triphosphate deaminase

Via homolog PDB 1xs1 UniProt P28248 Formula C₉H₁₅N₂O₁₄P₃
Mol. weight 468.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DUT
PDB
1xs1
UniProt (similar protein)
P28248
Target protein
VK055_5009

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 468.14 Da
LogP (Crippen) -1.47
H-bond donors 6
H-bond acceptors 11
TPSA 244.14 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 28
Fraction sp³ C 0.56
Formula C₉H₁₅N₂O₁₄P₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 244.1
  • −1 ≤ LogP ≤ 5 -1.47
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 468.1
  • LogP ≤ 5 -1.47
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 244.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C9H15N2O14P3/c12-5-3-8(11-2-1-7(13)10-9(11)14)23-6(5)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,20,21)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKey 
AHCYMLUZIRLXAA-SHYZEUOFSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF22769

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_5009.

PDB 5

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)