Ligand profile

7PM

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

Bound to: KP13_03124 — Dihydropteroate synthase type-1

Via homolog PDB 5u0z UniProt P0AC13 Formula C₁₃H₁₁N₅O₃S
Mol. weight 317.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7PM
PDB
5u0z
UniProt (similar protein)
P0AC13
Target protein
KP13_03124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 317.33 Da
LogP (Crippen) 1.15
H-bond donors 4
H-bond acceptors 6
TPSA 137.75 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 22
Fraction sp³ C 0.08
Formula C₁₃H₁₁N₅O₃S

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 137.7
  • −1 ≤ LogP ≤ 5 1.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 317.3
  • LogP ≤ 5 1.15
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 137.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)[C@H](C(=O)O)Sc2[nH]c3c(n2)C(=O)NC(=N3)N
InChI 
InChI=1S/C13H11N5O3S/c14-12-16-9-7(10(19)18-12)15-13(17-9)22-8(11(20)21)6-4-2-1-3-5-6/h1-5,8H,(H,20,21)(H4,14,15,16,17,18,19)/t8-/m1/s1
InChIKey 
CGEIBNIHDCYIDG-MRVPVSSYSA-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
PF00809

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_03124.

PDB 46

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

Ligand PDB entry

ChEMBL 26

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)