Ligand profile

R6Z

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

Bound to: KP13_03128 — Beta-lactamase CTX-M-2

Via homolog PDB 6oof UniProt Q9L5C7 Formula C₁₆H₁₀F₃N₉O
Mol. weight 401.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
R6Z
PDB
6oof
UniProt (similar protein)
Q9L5C7
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 401.31 Da
LogP (Crippen) 2.32
H-bond donors 3
H-bond acceptors 7
TPSA 138.02 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 29
Fraction sp³ C 0.06
Formula C₁₆H₁₀F₃N₉O

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 138.0
  • −1 ≤ LogP ≤ 5 2.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 401.3
  • LogP ≤ 5 2.32
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 138.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)NC(=O)c2cc(cc(c2)C(F)(F)F)c3[nH]nnn3)c4[nH]nnn4
InChI 
InChI=1S/C16H10F3N9O/c17-16(18,19)11-5-9(14-23-27-28-24-14)4-10(6-11)15(29)20-12-3-1-2-8(7-12)13-21-25-26-22-13/h1-7H,(H,20,29)(H,21,22,25,26)(H,23,24,27,28)
InChIKey 
JWIBBWSLVMIVLC-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
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_03128.

PDB 51

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

Ligand PDB entry

ChEMBL 6

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)