Ligand profile

3VN

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

Bound to: KP13_01654 — Dihydrodipicolinate synthase

Via homolog PDB 5f1u UniProt Q9PPB4 Formula C₁₄H₃₀N₄O₄
Mol. weight 318.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3VN
PDB
5f1u
UniProt (similar protein)
Q9PPB4
Target protein
KP13_01654

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 318.42 Da
LogP (Crippen) -0.41
H-bond donors 6
H-bond acceptors 6
TPSA 178.68 Ų
Rotatable bonds 13
Aromatic rings 0 / 0
Heavy atoms 22
Fraction sp³ C 0.86
Formula C₁₄H₃₀N₄O₄

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 178.7
  • −1 ≤ LogP ≤ 5 -0.41
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 318.4
  • LogP ≤ 5 -0.41
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 178.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCN)C[C@@](CC[C@](CCCCN)(C(=O)O)N)(C(=O)O)N
InChI 
InChI=1S/C14H30N4O4/c15-9-3-1-5-13(17,11(19)20)7-8-14(18,12(21)22)6-2-4-10-16/h1-10,15-18H2,(H,19,20)(H,21,22)/t13-,14-/m1/s1
InChIKey 
XYUHPPVEDOOPDE-ZIAGYGMSSA-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
PF00701

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_01654.

PDB 10

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)