Ligand profile

HM2

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog UniProt P53582 Formula C₁₈H₁₇ClN₄
pchembl 6.72 ~190.5 nM
Mol. weight 324.82 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HM2
UniProt (similar protein)
P53582
pchembl
6.720 (~190.5 nM)
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 324.82 Da
LogP (Crippen) 4.16
H-bond donors 1
H-bond acceptors 4
TPSA 50.70 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 23
Fraction sp³ C 0.17
Formula C₁₈H₁₇ClN₄

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 50.7
  • −1 ≤ LogP ≤ 5 4.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 324.8
  • LogP ≤ 5 4.16
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 50.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(nc(n1)c2ccccn2)NCCc3ccccc3)Cl
InChI 
InChI=1S/C18H17ClN4/c1-13-16(19)18(21-12-10-14-7-3-2-4-8-14)23-17(22-13)15-9-5-6-11-20-15/h2-9,11H,10,12H2,1H3,(H,21,22,23)
InChIKey 
HIUOABSWQSUEGK-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
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00557

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_2384.

PDB 46

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

Ligand PDB entry

ChEMBL 99

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)