Ligand profile

5AG

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

Bound to: KP13_02430 — putative inorganic polyphosphate/ATP-NAD kinase

Via homolog PDB 5dhs UniProt Q8Y8D7 Formula C₂₂H₂₃N₉O₄S
Mol. weight 509.55 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
5AG
PDB
5dhs
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 509.55 Da
LogP (Crippen) 0.77
H-bond donors 4
H-bond acceptors 11
TPSA 197.17 Ų
Rotatable bonds 9
Aromatic rings 3 / 4
Heavy atoms 36
Fraction sp³ C 0.36
Formula C₂₂H₂₃N₉O₄S

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 197.2
  • −1 ≤ LogP ≤ 5 0.77
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 509.6
  • LogP ≤ 5 0.77
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 197.2
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C#Cc1cccc(c1)CCNC(=O)CSc2nc3c(ncnc3n2C4C(C(C(O4)CN=[N+]=[N-])O)O)N
InChI 
InChI=1S/C22H23N9O4S/c1-2-12-4-3-5-13(8-12)6-7-25-15(32)10-36-22-29-16-19(23)26-11-27-20(16)31(22)21-18(34)17(33)14(35-21)9-28-30-24/h1,3-5,8,11,14,17-18,21,33-34H,6-7,9-10H2,(H,25,32)(H2,23,26,27)
InChIKey 
HEZMFPGXYOAFRQ-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
PF01513' 'PF20143

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_02430.

PDB 51

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

Ligand PDB entry

ChEMBL 3

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)