Ligand profile

PPS

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

Bound to: KP13_02403 — Adenylyl-sulfate kinase

Via homolog PDB 2ofx UniProt O43252 Formula C₁₀H₁₅N₅O₁₃P₂S
Mol. weight 507.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PPS
PDB
2ofx
UniProt (similar protein)
O43252
Target protein
KP13_02403

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 507.27 Da
LogP (Crippen) -1.92
H-bond donors 6
H-bond acceptors 14
TPSA 275.97 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.50
Formula C₁₀H₁₅N₅O₁₃P₂S

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 276.0
  • −1 ≤ LogP ≤ 5 -1.92
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 507.3
  • LogP ≤ 5 -1.92
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 276.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OS(=O)(=O)O)OP(=O)(O)O)O)N
InChI 
InChI=1S/C10H15N5O13P2S/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(27-29(17,18)19)4(26-10)1-25-30(20,21)28-31(22,23)24/h2-4,6-7,10,16H,1H2,(H,20,21)(H2,11,12,13)(H2,17,18,19)(H,22,23,24)/t4-,6-,7-,10-/m1/s1
InChIKey 
GACDQMDRPRGCTN-KQYNXXCUSA-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
PF01583

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_02403.

PDB 7

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)