Ligand profile

AKM

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

Bound to: VK055_0351 — acyl-CoA dehydrogenase, C-terminal domain protein

Via homolog PDB 4kcf UniProt B3TMR1 Formula C₁₇H₂₉N₃O₁₄P₂
Mol. weight 561.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AKM
PDB
4kcf
UniProt (similar protein)
B3TMR1
Target protein
VK055_0351

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 561.37 Da
LogP (Crippen) -1.72
H-bond donors 7
H-bond acceptors 14
TPSA 262.32 Ų
Rotatable bonds 8
Aromatic rings 1 / 3
Heavy atoms 36
Fraction sp³ C 0.76
Formula C₁₇H₂₉N₃O₁₄P₂

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 262.3
  • −1 ≤ LogP ≤ 5 -1.72
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 561.4
  • LogP ≤ 5 -1.72
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 262.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1C([C@@](C[C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)(C)N)(O)O
InChI 
InChI=1S/C17H29N3O14P2/c1-8-6-20(15(23)19-14(8)22)12-4-10(21)11(32-12)7-30-35(26,27)34-36(28,29)33-13-5-16(3,18)17(24,25)9(2)31-13/h6,9-13,21,24-25H,4-5,7,18H2,1-3H3,(H,26,27)(H,28,29)(H,19,22,23)/t9-,10+,11-,12-,13-,16+/m1/s1
InChIKey 
GACNZVKWDHTCBB-HHMBNNFFSA-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
PF00441' 'PF02770' 'PF02771' 'PF08028

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_0351.

PDB 4

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)