Ligand profile

NFF

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

Bound to: VK055_5052 — DD-carboxypeptidase, penicillin-binding protein 6b

Via homolog PDB 5ty2 UniProt A0A0H2WY27 Formula C₂₁H₂₄N₂O₅S
Mol. weight 416.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NFF
PDB
5ty2
UniProt (similar protein)
A0A0H2WY27
Target protein
VK055_5052

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 416.50 Da
LogP (Crippen) 2.43
H-bond donors 3
H-bond acceptors 6
TPSA 104.73 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.38
Formula C₂₁H₂₄N₂O₅S

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 104.7
  • −1 ≤ LogP ≤ 5 2.43
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 416.5
  • LogP ≤ 5 2.43
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 104.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCOc1ccc2ccccc2c1C(=O)N[C@H](C=O)[C@@H]3N[C@H](C(S3)(C)C)C(=O)O
InChI 
InChI=1S/C21H24N2O5S/c1-4-28-15-10-9-12-7-5-6-8-13(12)16(15)18(25)22-14(11-24)19-23-17(20(26)27)21(2,3)29-19/h5-11,14,17,19,23H,4H2,1-3H3,(H,22,25)(H,26,27)/t14-,17+,19-/m1/s1
InChIKey 
XDLYHUOUOKHAMD-DKSSEZFCSA-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' 'PF00768' 'PF09211

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_5052.

PDB 13

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

Ligand PDB entry

ChEMBL 1

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)