Ligand profile

SGV

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

Bound to: KP13_01981 — Chaperone protein dnaK

Via homolog PDB 5aqz UniProt P0DMV8 Formula C₁₂H₁₅N₅O₅
Mol. weight 309.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SGV
PDB
5aqz
UniProt (similar protein)
P0DMV8
Target protein
KP13_01981

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 309.28 Da
LogP (Crippen) -2.28
H-bond donors 5
H-bond acceptors 9
TPSA 169.74 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 22
Fraction sp³ C 0.42
Formula C₁₂H₁₅N₅O₅

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 169.7
  • −1 ≤ LogP ≤ 5 -2.28
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 309.3
  • LogP ≤ 5 -2.28
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 169.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N)C(=O)N
InChI 
InChI=1S/C12H15N5O5/c13-9-6-4(10(14)21)1-17(11(6)16-3-15-9)12-8(20)7(19)5(2-18)22-12/h1,3,5,7-8,12,18-20H,2H2,(H2,14,21)(H2,13,15,16)/t5-,7-,8-,12-/m1/s1
InChIKey 
OBZJZDHRXBKKTJ-JTFADIMSSA-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
PF00012

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_01981.

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)