Ligand profile

CB9

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

Bound to: KP13_00857 — Penicillin-binding protein 1C

Via homolog PDB 3zga UniProt Q8Y547 Formula C₁₇H₂₀N₂O₆S
Mol. weight 380.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CB9
PDB
3zga
UniProt (similar protein)
Q8Y547
Target protein
KP13_00857

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 380.42 Da
LogP (Crippen) 0.43
H-bond donors 4
H-bond acceptors 6
TPSA 132.80 Ų
Rotatable bonds 7
Aromatic rings 1 / 2
Heavy atoms 26
Fraction sp³ C 0.41
Formula C₁₇H₂₀N₂O₆S

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 132.8
  • −1 ≤ LogP ≤ 5 0.43
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 380.4
  • LogP ≤ 5 0.43
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 132.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@H](c2ccccc2)C(=O)O)C(=O)O)C
InChI 
InChI=1S/C17H20N2O6S/c1-17(2)12(16(24)25)19-14(26-17)10(8-20)18-13(21)11(15(22)23)9-6-4-3-5-7-9/h3-8,10-12,14,19H,1-2H3,(H,18,21)(H,22,23)(H,24,25)/t10-,11+,12+,14-/m1/s1
InChIKey 
YABPSSAFCROUQF-OWTLIXCDSA-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
PF00905

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_00857.

PDB 7

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

Ligand PDB entry

ChEMBL 7

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)