Ligand profile

CIR

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

Bound to: VK055_2800 — ornithine carbamoyltransferase

Via homolog PDB 4jqo UniProt Q8DCF5 Formula C₆H₁₃N₃O₃
Mol. weight 175.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CIR
PDB
4jqo
UniProt (similar protein)
Q8DCF5
Target protein
VK055_2800

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 175.19 Da
LogP (Crippen) -1.15
H-bond donors 4
H-bond acceptors 3
TPSA 118.44 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.67
Formula C₆H₁₃N₃O₃

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 118.4
  • −1 ≤ LogP ≤ 5 -1.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 175.2
  • LogP ≤ 5 -1.15
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 118.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C[C@@H](C(=O)O)N)CNC(=O)N
InChI 
InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12)/t4-/m0/s1
InChIKey 
RHGKLRLOHDJJDR-BYPYZUCNSA-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
PF00185' 'PF02729

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_2800.

PDB 14

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)