Ligand profile

B83

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 3il6 UniProt Q820T1 Formula C₂₇H₂₈N₂O₄
Mol. weight 444.53 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B83
PDB
3il6
UniProt (similar protein)
Q820T1
Target protein
VK055_1376

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 444.53 Da
LogP (Crippen) 5.91
H-bond donors 2
H-bond acceptors 4
TPSA 78.87 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.26
Formula C₂₇H₂₈N₂O₄

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 78.9
  • −1 ≤ LogP ≤ 5 5.91
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 444.5
  • LogP ≤ 5 5.91
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 78.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1C[C@@H](CN(C1)c2ccc(cc2Oc3ccccc3)C(=O)Nc4ccccc4C(=O)O)C
InChI 
InChI=1S/C27H28N2O4/c1-18-14-19(2)17-29(16-18)24-13-12-20(15-25(24)33-21-8-4-3-5-9-21)26(30)28-23-11-7-6-10-22(23)27(31)32/h3-13,15,18-19H,14,16-17H2,1-2H3,(H,28,30)(H,31,32)/t18-,19+
InChIKey 
YMZMFFRGSWCLPY-KDURUIRLSA-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
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)