Ligand profile

ZINC13552241

Virtual-screening candidate from ZINC.

Bound to: KP13_04789 — hypothetical protein

Via homolog UniProt Q6XGD8 Formula C₁₀H₁₆N₅O₁₂P₃
Tanimoto 0.60
Mol. weight 491.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13552241
UniProt (similar protein)
Q6XGD8
Tanimoto
0.600
Target protein
KP13_04789

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 491.18 Da
LogP (Crippen) -0.28
H-bond donors 6
H-bond acceptors 12
TPSA 258.64 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 30
Fraction sp³ C 0.50
Formula C₁₀H₁₆N₅O₁₂P₃

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 258.6
  • −1 ≤ LogP ≤ 5 -0.28
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 491.2
  • LogP ≤ 5 -0.28
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 258.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc(=O)c2ncn([C@@H]3CC[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O3)c2[nH]1
InChI 
InChI=1S/C10H16N5O12P3/c11-10-13-8-7(9(16)14-10)12-4-15(8)6-2-1-5(25-6)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h4-6H,1-3H2,(H,20,21)(H,22,23)(H2,17,18,19)(H3,11,13,14,16)/t5-,6+/m1/s1
InChIKey 
HDRRAMINWIWTNU-RITPCOANSA-N

Provenance

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

Method
LigQ sequence
Query
GH3
Homolog
Q6XGD8

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to KP13_04789.

PDB 5

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)