Ligand profile

Y3D

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

Bound to: KP13_02854 — Putrescine aminotransferase

Via homolog PDB 7lk0 UniProt P04181 Formula C₁₄H₁₇N₂O₈P
Mol. weight 372.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Y3D
PDB
7lk0
UniProt (similar protein)
P04181
Target protein
KP13_02854

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 372.27 Da
LogP (Crippen) 0.56
H-bond donors 4
H-bond acceptors 7
TPSA 166.61 Ų
Rotatable bonds 6
Aromatic rings 1 / 2
Heavy atoms 25
Fraction sp³ C 0.43
Formula C₁₄H₁₇N₂O₈P

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 166.6
  • −1 ≤ LogP ≤ 5 0.56
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 372.3
  • LogP ≤ 5 0.56
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 166.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H]2C[C@H](CC2=O)C(=O)O)O
InChI 
InChI=1S/C14H17N2O8P/c1-7-13(18)10(9(4-15-7)6-24-25(21,22)23)5-16-11-2-8(14(19)20)3-12(11)17/h4-5,8,11,18H,2-3,6H2,1H3,(H,19,20)(H2,21,22,23)/b16-5+/t8-,11+/m1/s1
InChIKey 
XLGFWCHBZWEILL-SNTOBFBISA-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
PF00202

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_02854.

PDB 12

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 4

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)