Ligand profile

B52

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

Bound to: KP13_03124 — Dihydropteroate synthase type-1

Via homolog PDB 3h21 UniProt Q81VW8 Formula C₁₀H₁₁N₅O₄
Mol. weight 265.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B52
PDB
3h21
UniProt (similar protein)
Q81VW8
Target protein
KP13_03124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 265.23 Da
LogP (Crippen) -1.21
H-bond donors 3
H-bond acceptors 7
TPSA 143.96 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 19
Fraction sp³ C 0.30
Formula C₁₀H₁₁N₅O₄

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 144.0
  • −1 ≤ LogP ≤ 5 -1.21
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 265.2
  • LogP ≤ 5 -1.21
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 144.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](C1=NN(C2=C(C1=O)C(=O)NC(=N2)N)C)C(=O)O
InChI 
InChI=1S/C10H11N5O4/c1-3(9(18)19)5-6(16)4-7(15(2)14-5)12-10(11)13-8(4)17/h3H,1-2H3,(H,18,19)(H3,11,12,13,17)/t3-/m1/s1
InChIKey 
XUKTUWRGSZSUGO-GSVOUGTGSA-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)