Ligand profile

3II

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

Bound to: KP13_31580 — Mercuric reductase

Via homolog PDB 3ii4 UniProt P9WHH9 Formula C₃₂H₃₄Cl₂N₄O₅
Mol. weight 625.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3II
PDB
3ii4
UniProt (similar protein)
P9WHH9
Target protein
KP13_31580

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 625.55 Da
LogP (Crippen) 4.65
H-bond donors 1
H-bond acceptors 6
TPSA 91.42 Ų
Rotatable bonds 9
Aromatic rings 3 / 5
Heavy atoms 43
Fraction sp³ C 0.34
Formula C₃₂H₃₄Cl₂N₄O₅

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 91.4
  • −1 ≤ LogP ≤ 5 4.65
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 625.6
  • LogP ≤ 5 4.65
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 91.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(c(c1)OC)C(=O)N2CCC3(CC2)C(=O)N(CN3c4ccccc4)CC(=O)NCCc5ccc(cc5Cl)Cl
InChI 
InChI=1S/C32H34Cl2N4O5/c1-42-25-10-11-26(28(19-25)43-2)30(40)36-16-13-32(14-17-36)31(41)37(21-38(32)24-6-4-3-5-7-24)20-29(39)35-15-12-22-8-9-23(33)18-27(22)34/h3-11,18-19H,12-17,20-21H2,1-2H3,(H,35,39)
InChIKey 
TWOVSEVREOPZGM-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
PF00070' 'PF02852' 'PF12831

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_31580.

PDB 17

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

Ligand PDB entry

ChEMBL 4

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)