Ligand profile

ZINC13540909

Virtual-screening candidate from ZINC.

Bound to: VK055_0231 — nitrite reductase [NAD(P)H], small subunit

Via homolog UniProt Q2FIA5 Formula C₁₀H₁₆N₅O₁₂P₃
Tanimoto 0.50
Mol. weight 491.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13540909
UniProt (similar protein)
Q2FIA5
Tanimoto
0.500
Target protein
VK055_0231

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 491.18 Da
LogP (Crippen) -0.60
H-bond donors 6
H-bond acceptors 13
TPSA 258.90 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 258.9
  • −1 ≤ LogP ≤ 5 -0.60
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 491.2
  • LogP ≤ 5 -0.60
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 258.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)C[C@H]1O
InChI 
InChI=1S/C10H16N5O12P3/c11-8-7-9(13-3-12-8)15(4-14-7)10-6(16)1-5(25-10)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-6,10,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,10+/m0/s1
InChIKey 
NLIHPCYXRYQPSD-BAJZRUMYSA-N

Provenance

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

Method
LigQ nearest_k
Query
CA6
Homolog
Q2FIA5

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_0231.

PDB 7

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

Ligand PDB entry

ZINC 25

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

Compound Similarity (Tanimoto)