Ligand profile

4VM

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

Bound to: VK055_1376 — 3-oxoacyl-[acyl-carrier-] synthase III family protein

Via homolog PDB 5bns UniProt P0A6R0 Formula C₂₈H₂₇FN₄O₂
Mol. weight 470.55 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4VM
PDB
5bns
UniProt (similar protein)
P0A6R0
Target protein
VK055_1376

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 470.55 Da
LogP (Crippen) 4.46
H-bond donors 2
H-bond acceptors 5
TPSA 78.35 Ų
Rotatable bonds 6
Aromatic rings 4 / 5
Heavy atoms 35
Fraction sp³ C 0.25
Formula C₂₈H₂₇FN₄O₂

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 78.4
  • −1 ≤ LogP ≤ 5 4.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 470.5
  • LogP ≤ 5 4.46
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 78.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2cc(ccc2nc1)CNC(=O)C3CCN(CC3)c4ccc(cn4)c5cc(ccc5F)CO
InChI 
InChI=1S/C28H27FN4O2/c29-25-6-3-20(18-34)15-24(25)23-5-8-27(31-17-23)33-12-9-21(10-13-33)28(35)32-16-19-4-7-26-22(14-19)2-1-11-30-26/h1-8,11,14-15,17,21,34H,9-10,12-13,16,18H2,(H,32,35)
InChIKey 
JBDGRQUVRNHGJF-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF08541' 'PF08545

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_1376.

PDB 14

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

Ligand PDB entry

ChEMBL 22

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)