Ligand profile

YH4

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

Bound to: VK055_2426 — 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase

Via homolog PDB 4m5l UniProt P26281 Formula C₁₄H₁₃N₅O₂S
Mol. weight 315.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
YH4
PDB
4m5l
UniProt (similar protein)
P26281
Target protein
VK055_2426

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 315.36 Da
LogP (Crippen) 1.51
H-bond donors 3
H-bond acceptors 6
TPSA 117.52 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 22
Fraction sp³ C 0.14
Formula C₁₄H₁₃N₅O₂S

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 117.5
  • −1 ≤ LogP ≤ 5 1.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 315.4
  • LogP ≤ 5 1.51
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 117.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccccc1C(=O)CSc2[nH]c3c(n2)N=C(NC3=O)N
InChI 
InChI=1S/C14H13N5O2S/c1-7-4-2-3-5-8(7)9(20)6-22-14-16-10-11(18-14)17-13(15)19-12(10)21/h2-5H,6H2,1H3,(H4,15,16,17,18,19,21)
InChIKey 
YXZULINHSYINAQ-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
PF01288

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2426.

PDB 27

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

Ligand PDB entry

ChEMBL 21

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)