Ligand profile

PMM

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

Bound to: KP13_03130 — Dihydropteroate synthase type-1

Via homolog PDB 1eye UniProt P9WND1 Formula C₇H₈N₅O₅P
Mol. weight 273.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PMM
PDB
1eye
UniProt (similar protein)
P9WND1
Target protein
KP13_03130

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 273.14 Da
LogP (Crippen) -1.10
H-bond donors 4
H-bond acceptors 7
TPSA 164.31 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 18
Fraction sp³ C 0.14
Formula C₇H₈N₅O₅P

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 164.3
  • −1 ≤ LogP ≤ 5 -1.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 273.1
  • LogP ≤ 5 -1.10
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 164.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(nc2c(n1)N=C(NC2=O)N)COP(=O)(O)O
InChI 
InChI=1S/C7H8N5O5P/c8-7-11-5-4(6(13)12-7)10-3(1-9-5)2-17-18(14,15)16/h1H,2H2,(H2,14,15,16)(H3,8,9,11,12,13)
InChIKey 
AJXFJEHKGGCFNM-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
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_03130.

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)