Ligand profile

5SR

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

Bound to: KP13_05584 — putative pyruvate-flavodoxin oxidoreductase

Via homolog PDB 5exe UniProt Q2RI41 Formula C₁₃H₁₈N₄O₉P₂S
Mol. weight 468.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5SR
PDB
5exe
UniProt (similar protein)
Q2RI41
Target protein
KP13_05584

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 468.32 Da
LogP (Crippen) -0.09
H-bond donors 4
H-bond acceptors 10
TPSA 209.10 Ų
Rotatable bonds 9
Aromatic rings 2 / 2
Heavy atoms 29
Fraction sp³ C 0.38
Formula C₁₃H₁₈N₄O₉P₂S

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 209.1
  • −1 ≤ LogP ≤ 5 -0.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 468.3
  • LogP ≤ 5 -0.09
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 209.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)O)CCOP(=O)(O)OP(=O)(O)[O-]
InChI 
InChI=1S/C13H18N4O9P2S/c1-7-10(3-4-25-28(23,24)26-27(20,21)22)29-12(13(18)19)17(7)6-9-5-15-8(2)16-11(9)14/h5H,3-4,6H2,1-2H3,(H5-,14,15,16,18,19,20,21,22,23,24)
InChIKey 
SXXTZHDPRYKKAS-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
PF01855' 'PF02775

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_05584.

PDB 5

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

Ligand PDB entry

ZINC 3

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

Compound Similarity (Tanimoto)