Ligand profile

ZINC5010885

Virtual-screening candidate from ZINC.

Bound to: VK055_3123 — biotin operon repressor

Via homolog UniProt O57883 Formula C₁₂H₁₇N₅O₄
Tanimoto 0.61
Mol. weight 295.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5010885
UniProt (similar protein)
O57883
Tanimoto
0.612
Target protein
VK055_3123

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 295.30 Da
LogP (Crippen) -1.92
H-bond donors 5
H-bond acceptors 9
TPSA 152.67 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 21
Fraction sp³ C 0.50
Formula C₁₂H₁₇N₅O₄

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 152.7
  • −1 ≤ LogP ≤ 5 -1.92
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 295.3
  • LogP ≤ 5 -1.92
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 152.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NCc1cn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c2ncnc(N)c12
InChI 
InChI=1S/C12H17N5O4/c13-1-5-2-17(11-7(5)10(14)15-4-16-11)12-9(20)8(19)6(3-18)21-12/h2,4,6,8-9,12,18-20H,1,3,13H2,(H2,14,15,16)/t6-,8+,9-,12+/m0/s1
InChIKey 
AFMKIRMZLLCSAV-UKHPNBTGSA-N

Provenance

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

Method
LigQ nearest_k
Query
ADN
Homolog
O57883

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_3123.

PDB 5

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

Ligand PDB entry

ChEMBL 2

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)