Ligand profile

DUP

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

Bound to: VK055_5009 — deoxycytidine triphosphate deaminase

Via homolog PDB 2hxd UniProt Q57872 Formula C₉H₁₆N₃O₁₃P₃
Mol. weight 467.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DUP
PDB
2hxd
UniProt (similar protein)
Q57872
Target protein
VK055_5009

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 467.16 Da
LogP (Crippen) -1.90
H-bond donors 7
H-bond acceptors 10
TPSA 246.94 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 28
Fraction sp³ C 0.56
Formula C₉H₁₆N₃O₁₃P₃

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 246.9
  • −1 ≤ LogP ≤ 5 -1.90
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 467.2
  • LogP ≤ 5 -1.90
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 246.9
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)(N[P@@](=O)(O)OP(=O)(O)O)O)O
InChI 
InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
InChIKey 
XZLLMTSKYYYJLH-SHYZEUOFSA-N

Provenance

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

Method
LigQ nearest_k
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)