Ligand profile

F6D

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

Bound to: VK055_3495 — pantetheine-phosphate adenylyltransferase

Via homolog PDB 6ckw UniProt P0A6I6 Formula C₂₄H₂₅ClN₈O
Mol. weight 476.97 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
F6D
PDB
6ckw
UniProt (similar protein)
P0A6I6
Target protein
VK055_3495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 476.97 Da
LogP (Crippen) 4.27
H-bond donors 3
H-bond acceptors 9
TPSA 126.18 Ų
Rotatable bonds 9
Aromatic rings 4 / 4
Heavy atoms 34
Fraction sp³ C 0.25
Formula C₂₄H₂₅ClN₈O

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 126.2
  • −1 ≤ LogP ≤ 5 4.27
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 477.0
  • LogP ≤ 5 4.27
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 126.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(n2c(n1)nc(n2)NC(CC#N)c3cccc(c3)Cl)NCC(c4ccccc4OC)N
InChI 
InChI=1S/C24H25ClN8O/c1-15-12-22(28-14-19(27)18-8-3-4-9-21(18)34-2)33-24(29-15)31-23(32-33)30-20(10-11-26)16-6-5-7-17(25)13-16/h3-9,12-13,19-20,28H,10,14,27H2,1-2H3,(H,30,32)
InChIKey 
TVYFBBBTUXLKKX-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)