Ligand profile

PDA

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

Bound to: KP13_03545 — Cysteine synthase B

Via homolog PDB 2q3d UniProt P9WP55 Formula C₁₁H₁₇N₂O₇P
Mol. weight 320.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PDA
PDB
2q3d
UniProt (similar protein)
P9WP55
Target protein
KP13_03545

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 320.24 Da
LogP (Crippen) 0.27
H-bond donors 5
H-bond acceptors 6
TPSA 149.21 Ų
Rotatable bonds 7
Aromatic rings 1 / 1
Heavy atoms 21
Fraction sp³ C 0.45
Formula C₁₁H₁₇N₂O₇P

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 149.2
  • −1 ≤ LogP ≤ 5 0.27
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 320.2
  • LogP ≤ 5 0.27
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 149.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)C(=O)O)O
InChI 
InChI=1S/C11H17N2O7P/c1-6-10(14)9(4-13-7(2)11(15)16)8(3-12-6)5-20-21(17,18)19/h3,7,13-14H,4-5H2,1-2H3,(H,15,16)(H2,17,18,19)
InChIKey 
WACJCHFWJNNBPR-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
PF00291

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_03545.

PDB 7

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

Ligand PDB entry

ChEMBL 15

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)