Ligand profile

POB

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

Bound to: KP13_01903 — D-alanine--D-alanine ligase B

Via homolog PDB 1iov UniProt P07862 Formula C₆H₁₅NO₈P₂
Mol. weight 291.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
POB
PDB
1iov
UniProt (similar protein)
P07862
Target protein
KP13_01903

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 291.13 Da
LogP (Crippen) 0.47
H-bond donors 4
H-bond acceptors 6
TPSA 156.38 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 17
Fraction sp³ C 0.83
Formula C₆H₁₅NO₈P₂

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 156.4
  • −1 ≤ LogP ≤ 5 0.47
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 291.1
  • LogP ≤ 5 0.47
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 156.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@H](C(=O)O)O[P@](=O)([C@@H](C)N)OP(=O)(O)O
InChI 
InChI=1S/C6H15NO8P2/c1-3-5(6(8)9)14-16(10,4(2)7)15-17(11,12)13/h4-5H,3,7H2,1-2H3,(H,8,9)(H2,11,12,13)/t4-,5+,16+/m0/s1
InChIKey 
LSPLWPXJPPQFJE-RJPXELBVSA-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
PF07478

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_01903.

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)