Ligand profile

8YF

Ligand co-crystallized with this exact protein (Protein Data Bank).

Bound to: KP13_06703 — Carbepenem-hydrolyzing beta-lactamase KPC2

Direct evidence PDB 6xj8 UniProt Q9F663 Formula C₁₂H₁₉N₃O₅S
Mol. weight 317.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8YF
PDB
6xj8
UniProt (this protein)
Q9F663
Target protein
KP13_06703

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 317.37 Da
LogP (Crippen) -0.34
H-bond donors 6
H-bond acceptors 6
TPSA 142.74 Ų
Rotatable bonds 9
Aromatic rings 0 / 1
Heavy atoms 21
Fraction sp³ C 0.58
Formula C₁₂H₁₉N₃O₅S

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 142.7
  • −1 ≤ LogP ≤ 5 -0.34
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 317.4
  • LogP ≤ 5 -0.34
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 142.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C/NCCSC1=C(N[C@H](C1)[C@@H]([C@@H](C)O)C(=O)O)C(=O)O
InChI 
InChI=1S/C12H19N3O5S/c1-6(16)9(11(17)18)7-4-8(10(15-7)12(19)20)21-3-2-14-5-13/h5-7,9,15-16H,2-4H2,1H3,(H2,13,14)(H,17,18)(H,19,20)/t6-,7-,9-/m1/s1
InChIKey 
KSLAOLVLEKIZMQ-ZXFLCMHBSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00144' 'PF13354

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_06703.

PDB 35

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

Ligand PDB entry

ChEMBL 100

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)