Ligand profile

2W2

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

Bound to: KP13_01017 — Lysine-arginine-ornithine-binding periplasmic protein

Via homolog PDB 5ovz UniProt P35120 Formula C₁₁H₂₀N₄O₆
Mol. weight 304.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2W2
PDB
5ovz
UniProt (similar protein)
P35120
Target protein
KP13_01017

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 304.30 Da
LogP (Crippen) -1.39
H-bond donors 7
H-bond acceptors 5
TPSA 185.83 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 21
Fraction sp³ C 0.64
Formula C₁₁H₂₀N₄O₆

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 185.8
  • −1 ≤ LogP ≤ 5 -1.39
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 304.3
  • LogP ≤ 5 -1.39
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 185.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](CCC(=O)O)C(=O)O
InChI 
InChI=1S/C11H20N4O6/c12-11(13)14-5-1-2-6(9(18)19)15-7(10(20)21)3-4-8(16)17/h6-7,15H,1-5H2,(H,16,17)(H,18,19)(H,20,21)(H4,12,13,14)/t6-,7+/m0/s1
InChIKey 
LMKYZBGVKHTLTN-NKWVEPMBSA-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
PF00497

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_01017.

PDB 7

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)