Ligand profile

SCB

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

Bound to: KP13_01799 — (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase

Via homolog PDB 2glm UniProt O25928 Formula C₂₄H₁₉ClN₂O₅S
Mol. weight 482.95 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
SCB
PDB
2glm
UniProt (similar protein)
O25928
Target protein
KP13_01799

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 482.95 Da
LogP (Crippen) 5.55
H-bond donors 1
H-bond acceptors 6
TPSA 92.34 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.12
Formula C₂₄H₁₉ClN₂O₅S

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 92.3
  • −1 ≤ LogP ≤ 5 5.55
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 482.9
  • LogP ≤ 5 5.55
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 92.3
PAINS Alert

Matches PAINS filter: ene_rhod_C(13). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COCCN1C(=O)C(=Cc2ccc(o2)c3ccc(c(c3)C(=O)O)Cl)SC1=Nc4ccccc4
InChI 
InChI=1S/C24H19ClN2O5S/c1-31-12-11-27-22(28)21(33-24(27)26-16-5-3-2-4-6-16)14-17-8-10-20(32-17)15-7-9-19(25)18(13-15)23(29)30/h2-10,13-14H,11-12H2,1H3,(H,29,30)
InChIKey 
BLYOIVXXTIAFFL-UHFFFAOYSA-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
PF07977

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_01799.

PDB 20

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

Ligand PDB entry

ChEMBL 5

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)