Ligand profile

ONS

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

Bound to: KP13_02169 — D-3-phosphoglycerate dehydrogenase

Via homolog PDB 6plg UniProt O43175 Formula C₂₆H₂₁Cl₂N₃O₄
Mol. weight 510.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ONS
PDB
6plg
UniProt (similar protein)
O43175
Target protein
KP13_02169

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 510.38 Da
LogP (Crippen) 4.75
H-bond donors 2
H-bond acceptors 5
TPSA 93.45 Ų
Rotatable bonds 6
Aromatic rings 4 / 5
Heavy atoms 35
Fraction sp³ C 0.19
Formula C₂₆H₂₁Cl₂N₃O₄

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 93.5
  • −1 ≤ LogP ≤ 5 4.75
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 510.4
  • LogP ≤ 5 4.75
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 93.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cn1c2ccc(c(c2cc1C(=O)NC3(COC3)c4ccc(cc4)[C@@H](c5cccnc5)C(=O)O)Cl)Cl
InChI 
InChI=1S/C26H21Cl2N3O4/c1-31-20-9-8-19(27)23(28)18(20)11-21(31)24(32)30-26(13-35-14-26)17-6-4-15(5-7-17)22(25(33)34)16-3-2-10-29-12-16/h2-12,22H,13-14H2,1H3,(H,30,32)(H,33,34)/t22-/m0/s1
InChIKey 
LHTXTAIWLHZCIX-QFIPXVFZSA-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
PF02826

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_02169.

PDB 19

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)