Ligand profile

31B

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

Bound to: VK055_0301 — proofreading thioesterase in enterobactin biosynthesis

Via homolog PDB 4qd9 UniProt Q9I3A4 Formula C₂₈H₃₉N₇O₁₅P₂
Mol. weight 775.60 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
31B
PDB
4qd9
UniProt (similar protein)
Q9I3A4
Target protein
VK055_0301

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 775.60 Da
LogP (Crippen) -0.79
H-bond donors 9
H-bond acceptors 17
TPSA 337.19 Ų
Rotatable bonds 18
Aromatic rings 3 / 4
Heavy atoms 52
Fraction sp³ C 0.50
Formula C₂₈H₃₉N₇O₁₅P₂

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 337.2
  • −1 ≤ LogP ≤ 5 -0.79
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 775.6
  • LogP ≤ 5 -0.79
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 18
  • TPSA ≤ 140 Ų 337.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(COP(=O)(O)OP(=O)(O)OC[C@H]1[C@H]([C@H]([C@H](O1)c2[nH]c3c(n2)c(ncn3)N)O)O)[C@H](C(=O)NCCC(=O)NCCOC(=O)c4ccccc4)O
InChI 
InChI=1S/C28H39N7O15P2/c1-28(2,22(39)26(40)31-9-8-17(36)30-10-11-46-27(41)15-6-4-3-5-7-15)13-48-52(44,45)50-51(42,43)47-12-16-19(37)20(38)21(49-16)25-34-18-23(29)32-14-33-24(18)35-25/h3-7,14,16,19-22,37-39H,8-13H2,1-2H3,(H,30,36)(H,31,40)(H,42,43)(H,44,45)(H3,29,32,33,34,35)/t16-,19+,20+,21-,22-/m0/s1
InChIKey 
KLLSEACSJWFZEP-NKRQLCBBSA-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
PF03061

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_0301.

PDB 8

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)