Ligand profile

8NB

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

Bound to: KP13_02169 — D-3-phosphoglycerate dehydrogenase

Via homolog PDB 5n53 UniProt O43175 Formula C₉H₁₀ClNO₂
Mol. weight 199.64 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8NB
PDB
5n53
UniProt (similar protein)
O43175
Target protein
KP13_02169

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 199.64 Da
LogP (Crippen) 2.31
H-bond donors 1
H-bond acceptors 2
TPSA 38.33 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 13
Fraction sp³ C 0.22
Formula C₉H₁₀ClNO₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 38.3
  • −1 ≤ LogP ≤ 5 2.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 199.6
  • LogP ≤ 5 2.31
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 38.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)Nc1ccc(c(c1)Cl)OC
InChI 
InChI=1S/C9H10ClNO2/c1-6(12)11-7-3-4-9(13-2)8(10)5-7/h3-5H,1-2H3,(H,11,12)
InChIKey 
WNOVNNUWOUKIOL-UHFFFAOYSA-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
PF00389' '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)