Ligand profile

ZINC31728964

Virtual-screening candidate from ZINC.

Bound to: VK055_3123 — biotin operon repressor

Via homolog UniProt O57883 Formula C₁₁H₁₃ClN₄O₄
Tanimoto 0.60
Mol. weight 300.70 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC31728964
UniProt (similar protein)
O57883
Tanimoto
0.600
Target protein
VK055_3123

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 300.70 Da
LogP (Crippen) -0.72
H-bond donors 4
H-bond acceptors 8
TPSA 126.65 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.45
Formula C₁₁H₁₃ClN₄O₄

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 126.7
  • −1 ≤ LogP ≤ 5 -0.72
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 300.7
  • LogP ≤ 5 -0.72
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 126.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1cc(Cl)c2ncn([C@H]3O[C@@H](CO)[C@@H](O)[C@@H]3O)c2n1
InChI 
InChI=1S/C11H13ClN4O4/c12-4-1-6(13)15-10-7(4)14-3-16(10)11-9(19)8(18)5(2-17)20-11/h1,3,5,8-9,11,17-19H,2H2,(H2,13,15)/t5-,8+,9-,11-/m0/s1
InChIKey 
YBYUQJYDWFXQDB-YQRDOJIBSA-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)