Ligand profile

Y01

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

Bound to: KP13_15122 — Arabinose-proton symporter

Via homolog PDB 5c65 UniProt P11169 Formula C₃₁H₅₀O₄
Mol. weight 486.74 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Y01
PDB
5c65
UniProt (similar protein)
P11169
Target protein
KP13_15122

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 486.74 Da
LogP (Crippen) 7.80
H-bond donors 1
H-bond acceptors 3
TPSA 63.60 Ų
Rotatable bonds 9
Aromatic rings 0 / 4
Heavy atoms 35
Fraction sp³ C 0.87
Formula C₃₁H₅₀O₄

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 63.6
  • −1 ≤ LogP ≤ 5 7.80
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 486.7
  • LogP ≤ 5 7.80
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 63.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)OC(=O)CCC(=O)O)C)C
InChI 
InChI=1S/C31H50O4/c1-20(2)7-6-8-21(3)25-11-12-26-24-10-9-22-19-23(35-29(34)14-13-28(32)33)15-17-30(22,4)27(24)16-18-31(25,26)5/h9,20-21,23-27H,6-8,10-19H2,1-5H3,(H,32,33)/t21-,23+,24+,25-,26+,27+,30+,31-/m1/s1
InChIKey 
WLNARFZDISHUGS-MIXBDBMTSA-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
PF00083

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_15122.

PDB 3

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

Ligand PDB entry

ChEMBL 100

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)