Ligand profile

NIC

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

Bound to: KP13_05339 — Aconitate hydratase 1

Via homolog PDB 8acn UniProt P20004 Formula C₅H₇NO₇
Mol. weight 193.11 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NIC
PDB
8acn
UniProt (similar protein)
P20004
Target protein
KP13_05339

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 193.11 Da
LogP (Crippen) -1.45
H-bond donors 3
H-bond acceptors 5
TPSA 137.97 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.60
Formula C₅H₇NO₇

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 138.0
  • −1 ≤ LogP ≤ 5 -1.45
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 193.1
  • LogP ≤ 5 -1.45
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 138.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]([C@H](C(=O)O)O)[N+](=O)[O-])C(=O)O
InChI 
InChI=1S/C5H7NO7/c7-3(8)1-2(6(12)13)4(9)5(10)11/h2,4,9H,1H2,(H,7,8)(H,10,11)/t2-,4+/m0/s1
InChIKey 
ZTJSGPUFCRRTOT-ZAFYKAAXSA-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
PF00330' 'PF00694

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_05339.

PDB 10

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

Ligand PDB entry

ZINC 14

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)