Ligand profile

3BH

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

Bound to: KP13_01981 — Chaperone protein dnaK

Via homolog PDB 6dfm UniProt P11021 Formula C₁₀H₁₄N₆O₄
Mol. weight 282.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3BH
PDB
6dfm
UniProt (similar protein)
P11021
Target protein
KP13_01981

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 282.26 Da
LogP (Crippen) -2.40
H-bond donors 5
H-bond acceptors 10
TPSA 165.56 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.50
Formula C₁₀H₁₄N₆O₄

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 165.6
  • −1 ≤ LogP ≤ 5 -2.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 282.3
  • LogP ≤ 5 -2.40
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 165.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(c(n2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N
InChI 
InChI=1S/C10H14N6O4/c11-7-4-8(14-2-13-7)16(10(12)15-4)9-6(19)5(18)3(1-17)20-9/h2-3,5-6,9,17-19H,1H2,(H2,12,15)(H2,11,13,14)/t3-,5-,6-,9-/m1/s1
InChIKey 
DVGWFQILDUEEGX-UUOKFMHZSA-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)