Ligand profile

EXP

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

Bound to: VK055_3495 — pantetheine-phosphate adenylyltransferase

Via homolog PDB 6ccm UniProt P0A6I6 Formula C₁₃H₁₂BrN₅O
Mol. weight 334.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EXP
PDB
6ccm
UniProt (similar protein)
P0A6I6
Target protein
VK055_3495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 334.18 Da
LogP (Crippen) 2.79
H-bond donors 1
H-bond acceptors 6
TPSA 72.17 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.23
Formula C₁₃H₁₂BrN₅O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 72.2
  • −1 ≤ LogP ≤ 5 2.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 334.2
  • LogP ≤ 5 2.79
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 72.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=Nc2nc(nn2C(=O)C1)NCc3cccc(c3)Br
InChI 
InChI=1S/C13H12BrN5O/c1-8-5-11(20)19-13(16-8)17-12(18-19)15-7-9-3-2-4-10(14)6-9/h2-4,6H,5,7H2,1H3,(H,15,18)
InChIKey 
NONMKRIVUVFGSW-UHFFFAOYSA-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)