Ligand profile

NAK

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

Bound to: KP13_02757 — Cystathionine beta-lyase

Via homolog PDB 4iyo UniProt Q5H4T8 Formula C₃H₅NO₂
Mol. weight 87.08 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NAK
PDB
4iyo
UniProt (similar protein)
Q5H4T8
Target protein
KP13_02757

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 87.08 Da
LogP (Crippen) -3.04
H-bond donors 1
H-bond acceptors 2
TPSA 65.72 Ų
Rotatable bonds 1
Aromatic rings 0 / 0
Heavy atoms 6
Fraction sp³ C 0.33
Formula C₃H₅NO₂

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 65.7
  • −1 ≤ LogP ≤ 5 -3.04
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 87.1
  • LogP ≤ 5 -3.04
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 65.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=[NH2+])C(=O)[O-]
InChI 
InChI=1S/C3H5NO2/c1-2(4)3(5)6/h4H,1H3,(H,5,6)
InChIKey 
DUAWRLXHCUAWMK-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
PF01053

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_02757.

PDB 5

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

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 24

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)