Ligand profile

HDE

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

Bound to: KP13_05384 — Catalase HPII

Via homolog PDB 3p9q UniProt P21179 Formula C₃₄H₃₈FeN₄O₅
Mol. weight 638.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HDE
PDB
3p9q
UniProt (similar protein)
P21179
Target protein
KP13_05384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 638.55 Da
LogP (Crippen) 4.58
H-bond donors 2
H-bond acceptors 8
TPSA 101.86 Ų
Rotatable bonds 5
Aromatic rings 3 / 9
Heavy atoms 44
Fraction sp³ C 0.47
Formula C₃₄H₃₈FeN₄O₅

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 101.9
  • −1 ≤ LogP ≤ 5 4.58
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 638.5
  • LogP ≤ 5 4.58
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 101.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCc1c(c2n3c1Cc4c(c(c5n4[Fe]36n7c(c(c(c7C=C8N6C(=C5)[C@@]9([C@@]8(C)O)CCC(=O)O9)C)CC)C2)CCC(=O)O)C)C
InChI 
InChI=1S/C34H38N4O5.Fe/c1-7-20-17(3)23-13-27-21(8-2)18(4)25(37-27)15-29-33(6,42)34(12-11-32(41)43-34)30(38-29)16-28-22(9-10-31(39)40)19(5)24(36-28)14-26(20)35-23;/h15-16,42H,7-14H2,1-6H3,(H,39,40);/q-4;+4/t33-,34+;/m0./s1
InChIKey 
SQSYUADQFVTXKU-XCVPDAMTSA-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
PF00199

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_05384.

PDB 7

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)