Ligand profile

ELN

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

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog PDB 6g30 UniProt P55072 Formula C₉H₇ClN₂O
Mol. weight 194.62 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ELN
PDB
6g30
UniProt (similar protein)
P55072
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 194.62 Da
LogP (Crippen) 2.19
H-bond donors 1
H-bond acceptors 2
TPSA 52.89 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 13
Fraction sp³ C 0.11
Formula C₉H₇ClN₂O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 52.9
  • −1 ≤ LogP ≤ 5 2.19
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 194.6
  • LogP ≤ 5 2.19
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 52.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1NC(=O)CC#N)Cl
InChI 
InChI=1S/C9H7ClN2O/c10-7-1-3-8(4-2-7)12-9(13)5-6-11/h1-4H,5H2,(H,12,13)
InChIKey 
FLLVVAHFEBGZKD-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
PF00004

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_0072.

PDB 8

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

Ligand PDB entry

ChEMBL 100

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)