Ligand profile

ZINC5011208

Virtual-screening candidate from ZINC.

Bound to: KP13_04211 — Seryl-tRNA synthetase

Via homolog UniProt P0A8L1 Formula C₁₁H₁₃N₅O₅
Tanimoto 0.59
Mol. weight 295.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5011208
UniProt (similar protein)
P0A8L1
Tanimoto
0.594
Target protein
KP13_04211

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 295.25 Da
LogP (Crippen) -1.80
H-bond donors 3
H-bond acceptors 10
TPSA 145.61 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 21
Fraction sp³ C 0.45
Formula C₁₁H₁₃N₅O₅

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 145.6
  • −1 ≤ LogP ≤ 5 -1.80
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 295.3
  • LogP ≤ 5 -1.80
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 145.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COC=O)[C@@H](O)[C@@H]1O
InChI 
InChI=1S/C11H13N5O5/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(19)7(18)5(21-11)1-20-4-17/h2-5,7-8,11,18-19H,1H2,(H2,12,13,14)/t5-,7+,8-,11+/m0/s1
InChIKey 
DZKSMXWWERZQLU-IZCITBFLSA-N

Provenance

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

Method
LigQ sequence
Query
SSA
Homolog
P0A8L1

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_04211.

PDB 4

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

Ligand PDB entry

ChEMBL 4

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)