Ligand profile

7RM

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

Bound to: KP13_00433 — Acetyl-coenzyme A synthetase

Via homolog PDB 5u29 UniProt J9VFT1 Formula C₁₂H₁₆N₆O₇S
Mol. weight 388.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7RM
PDB
5u29
UniProt (similar protein)
J9VFT1
Target protein
KP13_00433

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 388.36 Da
LogP (Crippen) -2.57
H-bond donors 4
H-bond acceptors 12
TPSA 191.78 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.50
Formula C₁₂H₁₆N₆O₇S

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 191.8
  • −1 ≤ LogP ≤ 5 -2.57
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 388.4
  • LogP ≤ 5 -2.57
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 191.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
InChI 
InChI=1S/C12H16N6O7S/c1-5(19)17-26(22,23)24-2-6-8(20)9(21)12(25-6)18-4-16-7-10(13)14-3-15-11(7)18/h3-4,6,8-9,12,20-21H,2H2,1H3,(H,17,19)(H2,13,14,15)/t6-,8-,9-,12-/m1/s1
InChIKey 
SKYBLZMECJREBK-WOUKDFQISA-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
PF00501

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_00433.

PDB 4

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)