Ligand profile

DAR

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

Bound to: KP13_00617 — D-tyrosyl-tRNA(Tyr) deacylase

Via homolog PDB 3ko9 UniProt Q8IIS0 Formula C₆H₁₅N₄O₂⁺
Mol. weight 175.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DAR
PDB
3ko9
UniProt (similar protein)
Q8IIS0
Target protein
KP13_00617

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 175.21 Da
LogP (Crippen) -3.16
H-bond donors 5
H-bond acceptors 2
TPSA 126.96 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.67
Formula C₆H₁₅N₄O₂⁺

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 127.0
  • −1 ≤ LogP ≤ 5 -3.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 175.2
  • LogP ≤ 5 -3.16
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 127.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C[C@H](C(=O)O)N)CNC(=[NH2+])N
InChI 
InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m1/s1
InChIKey 
ODKSFYDXXFIFQN-SCSAIBSYSA-O

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
PF02580

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_00617.

PDB 3

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)