Ligand profile

5RZ

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

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

Via homolog PDB 5etv UniProt Q2G0Q5 Formula C₁₃H₁₀BrN₅O₂S
Mol. weight 380.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5RZ
PDB
5etv
UniProt (similar protein)
Q2G0Q5
Target protein
VK055_2426

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 380.23 Da
LogP (Crippen) 1.97
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 0.08
Formula C₁₃H₁₀BrN₅O₂S

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 1.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 380.2
  • LogP ≤ 5 1.97
  • 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 
c1cc(ccc1C(=O)CSc2[nH]c3c(n2)C(=O)NC(=N3)N)Br
InChI 
InChI=1S/C13H10BrN5O2S/c14-7-3-1-6(2-4-7)8(20)5-22-13-16-9-10(18-13)17-12(15)19-11(9)21/h1-4H,5H2,(H4,15,16,17,18,19,21)
InChIKey 
NIDWVLLSHNTXJV-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)