Ligand profile

EXS

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

Bound to: VK055_3495 — pantetheine-phosphate adenylyltransferase

Via homolog PDB 6ccn UniProt P0A6I6 Formula C₁₅H₂₁N₃O₄
Mol. weight 307.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EXS
PDB
6ccn
UniProt (similar protein)
P0A6I6
Target protein
VK055_3495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 307.35 Da
LogP (Crippen) 0.31
H-bond donors 5
H-bond acceptors 5
TPSA 118.47 Ų
Rotatable bonds 6
Aromatic rings 2 / 2
Heavy atoms 22
Fraction sp³ C 0.47
Formula C₁₅H₂₁N₃O₄

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 118.5
  • −1 ≤ LogP ≤ 5 0.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 307.4
  • LogP ≤ 5 0.31
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 118.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CO)[C@H](C(=O)NCCc1[nH]c2c(n1)cccc2O)O
InChI 
InChI=1S/C15H21N3O4/c1-15(2,8-19)13(21)14(22)16-7-6-11-17-9-4-3-5-10(20)12(9)18-11/h3-5,13,19-21H,6-8H2,1-2H3,(H,16,22)(H,17,18)/t13-/m0/s1
InChIKey 
SKIDJNQZVCDYIE-ZDUSSCGKSA-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
PF01467

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_3495.

PDB 21

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)