Ligand profile

FMC

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

Bound to: VK055_2391 — MTA/SAH nucleosidase

Via homolog PDB 1nc3 UniProt P0AF12 Formula C₁₀H₁₃N₅O₄
Mol. weight 267.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FMC
PDB
1nc3
UniProt (similar protein)
P0AF12
Target protein
VK055_2391

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 267.25 Da
LogP (Crippen) -1.91
H-bond donors 5
H-bond acceptors 8
TPSA 150.40 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.50
Formula C₁₀H₁₃N₅O₄

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 150.4
  • −1 ≤ LogP ≤ 5 -1.91
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 267.2
  • LogP ≤ 5 -1.91
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 150.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(c(n1)N)[nH]nc2[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
InChI 
InChI=1S/C10H13N5O4/c11-10-6-4(12-2-13-10)5(14-15-6)9-8(18)7(17)3(1-16)19-9/h2-3,7-9,16-18H,1H2,(H,14,15)(H2,11,12,13)/t3-,7-,8-,9+/m1/s1
InChIKey 
KBHMEHLJSZMEMI-KSYZLYKTSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF01048

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_2391.

PDB 10

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

Ligand PDB entry

ChEMBL 34

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)