Ligand profile

N3G

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_3123 — biotin operon repressor

Via homolog PDB 6oru UniProt A0A3A5LBF0 Formula C₁₉H₂₉N₉O₄S₂
Mol. weight 511.63 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
N3G
PDB
6oru
UniProt (similar protein)
A0A3A5LBF0
Target protein
VK055_3123

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 511.63 Da
LogP (Crippen) -0.13
H-bond donors 5
H-bond acceptors 10
TPSA 186.02 Ų
Rotatable bonds 12
Aromatic rings 2 / 4
Heavy atoms 34
Fraction sp³ C 0.63
Formula C₁₉H₂₉N₉O₄S₂

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 186.0
  • −1 ≤ LogP ≤ 5 -0.13
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 511.6
  • LogP ≤ 5 -0.13
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 186.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)CCCCNS(=O)(=O)NC(=O)CCCC[C@H]3[C@@H]4[C@H](CS3)NC(=O)N4)N
InChI 
InChI=1S/C19H29N9O4S2/c20-17-16-18(22-10-21-17)28(11-23-16)8-4-3-7-24-34(31,32)27-14(29)6-2-1-5-13-15-12(9-33-13)25-19(30)26-15/h10-13,15,24H,1-9H2,(H,27,29)(H2,20,21,22)(H2,25,26,30)/t12-,13-,15-/m0/s1
InChIKey 
WPCYKZJXLXIRGW-YDHLFZDLSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF03099

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 4

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 50

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

Compound Similarity (Tanimoto)