Ligand profile

CHEMBL5288850

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_2481 — phospho-N-acetylmuramoyl-pentapeptide- transferase

Via homolog UniProt P0A6W3 Formula C₂₄H₄₂N₄O₉
pchembl 6.48 ~331.1 nM
Mol. weight 530.62 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5288850
UniProt (similar protein)
P0A6W3
pchembl
6.480 (~331.1 nM)
Target protein
VK055_2481

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 530.62 Da
LogP (Crippen) -1.71
H-bond donors 7
H-bond acceptors 12
TPSA 201.52 Ų
Rotatable bonds 15
Aromatic rings 1 / 3
Heavy atoms 37
Fraction sp³ C 0.83
Formula C₂₄H₄₂N₄O₉

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 201.5
  • −1 ≤ LogP ≤ 5 -1.71
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 530.6
  • LogP ≤ 5 -1.71
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 201.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCNCC(O[C@@H]1O[C@H](CN)[C@@H](O)[C@H]1O)[C@H]1O[C@@H](n2ccc(=O)[nH]c2=O)[C@H](O)[C@@H]1O
InChI 
InChI=1S/C24H42N4O9/c1-2-3-4-5-6-7-8-10-26-13-15(36-23-20(33)17(30)14(12-25)35-23)21-18(31)19(32)22(37-21)28-11-9-16(29)27-24(28)34/h9,11,14-15,17-23,26,30-33H,2-8,10,12-13,25H2,1H3,(H,27,29,34)/t14-,15?,17-,18+,19-,20-,21-,22-,23+/m1/s1
InChIKey 
OBRVJALUYHKEOH-RYEZTZEQSA-N

Provenance

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

Method
LigQ sequence
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00953' 'PF10555

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_2481.

PDB 2

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

Ligand PDB entry

ChEMBL 34

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)