Ligand profile

3FD

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

Bound to: KP13_01981 — Chaperone protein dnaK

Via homolog PDB 6cz1 UniProt P11021 Formula C₂₅H₂₃Cl₂N₇O₄
Mol. weight 556.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3FD
PDB
6cz1
UniProt (similar protein)
P11021
Target protein
KP13_01981

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 556.41 Da
LogP (Crippen) 3.04
H-bond donors 4
H-bond acceptors 11
TPSA 164.36 Ų
Rotatable bonds 8
Aromatic rings 4 / 5
Heavy atoms 38
Fraction sp³ C 0.28
Formula C₂₅H₂₃Cl₂N₇O₄

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 164.4
  • −1 ≤ LogP ≤ 5 3.04
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 556.4
  • LogP ≤ 5 3.04
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 164.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1COCC2C(C(C(O2)n3c4c(c(ncn4)N)nc3NCc5ccc(c(c5)Cl)Cl)O)O)C#N
InChI 
InChI=1S/C25H23Cl2N7O4/c26-16-6-5-15(7-17(16)27)9-30-25-33-19-22(29)31-12-32-23(19)34(25)24-21(36)20(35)18(38-24)11-37-10-14-3-1-13(8-28)2-4-14/h1-7,12,18,20-21,24,35-36H,9-11H2,(H,30,33)(H2,29,31,32)
InChIKey 
ZXGGCBQORXDVTE-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
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)