Ligand profile

3MW

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

Bound to: VK055_4646 — aminopeptidase B

Via homolog PDB 4r7m UniProt Q8IL11 Formula C₁₈H₁₇N₅O₃
Mol. weight 351.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3MW
PDB
4r7m
UniProt (similar protein)
Q8IL11
Target protein
VK055_4646

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 351.37 Da
LogP (Crippen) 1.43
H-bond donors 4
H-bond acceptors 6
TPSA 122.27 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.06
Formula C₁₈H₁₇N₅O₃

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 122.3
  • −1 ≤ LogP ≤ 5 1.43
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 351.4
  • LogP ≤ 5 1.43
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 122.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cnn(c1)c2ccc(cc2)[C@H](C(=O)NO)NC(=O)c3ccc(cc3)N
InChI 
InChI=1S/C18H17N5O3/c19-14-6-2-13(3-7-14)17(24)21-16(18(25)22-26)12-4-8-15(9-5-12)23-11-1-10-20-23/h1-11,16,26H,19H2,(H,21,24)(H,22,25)/t16-/m1/s1
InChIKey 
XHKYHEBAKPKAIX-MRXNPFEDSA-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
PF00883

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_4646.

PDB 9

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)