Ligand profile

D17

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

Bound to: VK055_2476 — UDP-N-acetylmuramate--alanine ligase

Via homolog PDB 2wjp UniProt P14900 Formula C₂₃H₂₁N₃O₆S₂
Mol. weight 499.57 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
D17
PDB
2wjp
UniProt (similar protein)
P14900
Target protein
VK055_2476

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 499.57 Da
LogP (Crippen) 2.84
H-bond donors 5
H-bond acceptors 7
TPSA 144.83 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 34
Fraction sp³ C 0.17
Formula C₂₃H₂₁N₃O₆S₂

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 144.8
  • −1 ≤ LogP ≤ 5 2.84
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 499.6
  • LogP ≤ 5 2.84
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 144.8
PAINS Alert

Matches PAINS filter: ene_rhod_A(235). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)C(=O)N[C@@H](CCC(=O)O)C(=O)O)CNc2ccc(cc2)\C=C/3\C(=O)NC(=S)S3
InChI 
InChI=1S/C23H21N3O6S2/c27-19(28)9-8-17(22(31)32)25-20(29)15-3-1-2-14(10-15)12-24-16-6-4-13(5-7-16)11-18-21(30)26-23(33)34-18/h1-7,10-11,17,24H,8-9,12H2,(H,25,29)(H,27,28)(H,31,32)(H,26,30,33)/b18-11-/t17-/m0/s1
InChIKey 
ISIOCNFLEMFKTN-PBXDPIQXSA-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
PF02875' 'PF08245' 'PF21799

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_2476.

PDB 17

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)