Ligand profile

VMX

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

Bound to: KP13_31805 — Sulfur carrier protein ThiS adenylyltransferase

Via homolog PDB 6o83 UniProt O94609 Formula C₁₃H₂₁N₇O₅S
Mol. weight 387.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VMX
PDB
6o83
UniProt (similar protein)
O94609
Target protein
KP13_31805

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 387.42 Da
LogP (Crippen) -2.70
H-bond donors 5
H-bond acceptors 11
TPSA 191.50 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.62
Formula C₁₃H₂₁N₇O₅S

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 191.5
  • −1 ≤ LogP ≤ 5 -2.70
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 387.4
  • LogP ≤ 5 -2.70
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 191.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CNS(=O)(=O)CCCN)O)O)N
InChI 
InChI=1S/C13H21N7O5S/c14-2-1-3-26(23,24)19-4-7-9(21)10(22)13(25-7)20-6-18-8-11(15)16-5-17-12(8)20/h5-7,9-10,13,19,21-22H,1-4,14H2,(H2,15,16,17)/t7-,9-,10-,13-/m1/s1
InChIKey 
GCNSCCULRVBOML-QYVSTXNMSA-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
PF00899

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_31805.

PDB 8

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

Ligand PDB entry

ChEMBL 30

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)