Ligand profile

B53

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

Bound to: KP13_03130 — Dihydropteroate synthase type-1

Via homolog PDB 3h22 UniProt Q81VW8 Formula C₄H₅N₅O₂
Mol. weight 155.12 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B53
PDB
3h22
UniProt (similar protein)
Q81VW8
Target protein
KP13_03130

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 155.12 Da
LogP (Crippen) -0.67
H-bond donors 3
H-bond acceptors 6
TPSA 127.22 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 11
Fraction sp³ C 0.00
Formula C₄H₅N₅O₂

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 127.2
  • −1 ≤ LogP ≤ 5 -0.67
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 155.1
  • LogP ≤ 5 -0.67
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 127.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1(=C(N=C(NC1=O)N)N)N=O
InChI 
InChI=1S/C4H5N5O2/c5-2-1(9-11)3(10)8-4(6)7-2/h(H5,5,6,7,8,10)
InChIKey 
HVMRLFSFHWCUCG-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)