Ligand profile

5A8

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

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

Via homolog PDB 5dhu UniProt Q8Y8D7 Formula C₂₂H₂₄N₁₀O₄S
Mol. weight 524.57 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
5A8
PDB
5dhu
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 524.57 Da
LogP (Crippen) 1.27
H-bond donors 5
H-bond acceptors 11
TPSA 212.96 Ų
Rotatable bonds 9
Aromatic rings 4 / 5
Heavy atoms 37
Fraction sp³ C 0.36
Formula C₂₂H₂₄N₁₀O₄S

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 213.0
  • −1 ≤ LogP ≤ 5 1.27
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 524.6
  • LogP ≤ 5 1.27
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 213.0
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 
c1ccc2c(c1)c(c[nH]2)CCNC(=O)CSc3nc4c(ncnc4n3[C@H]5[C@@H]([C@@H]([C@H](O5)CN=[N+]=[N-])O)O)N
InChI 
InChI=1S/C22H24N10O4S/c23-19-16-20(28-10-27-19)32(21-18(35)17(34)14(36-21)8-29-31-24)22(30-16)37-9-15(33)25-6-5-11-7-26-13-4-2-1-3-12(11)13/h1-4,7,10,14,17-18,21,26,34-35H,5-6,8-9H2,(H,25,33)(H2,23,27,28)/t14-,17-,18-,21-/m1/s1
InChIKey 
NZVSVIHQZMZCNV-HAXDFEGKSA-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
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)