Ligand profile

ZINC13516025

Virtual-screening candidate from ZINC.

Bound to: KP13_02537 — putative DNA helicase

Via homolog UniProt P51530 Formula C₉H₁₆N₃O₁₅P₃
Tanimoto 0.66
Mol. weight 499.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13516025
UniProt (similar protein)
P51530
Tanimoto
0.655
Target protein
KP13_02537

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 499.16 Da
LogP (Crippen) -1.99
H-bond donors 8
H-bond acceptors 14
TPSA 276.66 Ų
Rotatable bonds 9
Aromatic rings 1 / 2
Heavy atoms 30
Fraction sp³ C 0.56
Formula C₉H₁₆N₃O₁₅P₃

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 276.7
  • −1 ≤ LogP ≤ 5 -1.99
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 499.2
  • LogP ≤ 5 -1.99
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 276.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=c1nc(NO)ccn1[C@@H]1O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C9H16N3O15P3/c13-6-4(3-24-29(20,21)27-30(22,23)26-28(17,18)19)25-8(7(6)14)12-2-1-5(11-16)10-9(12)15/h1-2,4,6-8,13-14,16H,3H2,(H,20,21)(H,22,23)(H,10,11,15)(H2,17,18,19)/t4-,6-,7-,8-/m1/s1
InChIKey 
BNIQIYMICUFERK-XVFCMESISA-N

Provenance

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

Method
LigQ nearest_k
Query
CHEMBL336296
Homolog
P51530

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_02537.

PDB 3

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

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

Compound Similarity (Tanimoto)