Ligand profile

H02

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

Bound to: KP13_03616 — Ferrochelatase

Via homolog PDB 2q3j UniProt P32396 Formula C₃₅H₄₂N₄O₄
Mol. weight 582.75 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
H02
PDB
2q3j
UniProt (similar protein)
P32396
Target protein
KP13_03616

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 582.75 Da
LogP (Crippen) 3.03
H-bond donors 5
H-bond acceptors 3
TPSA 126.90 Ų
Rotatable bonds 8
Aromatic rings 4 / 5
Heavy atoms 43
Fraction sp³ C 0.37
Formula C₃₅H₄₂N₄O₄

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 126.9
  • −1 ≤ LogP ≤ 5 3.03
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 582.7
  • LogP ≤ 5 3.03
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 126.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCc1c(c\2[nH]c1C=C3C(=C(C(=Cc4c(c(c([nH]4)C=C5C(=C(/C(=C2)/N5)C)CCC(=O)O)CCC(=O)O)C)N3C)CC)C)C
InChI 
InChI=1S/C35H42N4O4/c1-8-22-18(3)26-14-27-19(4)24(10-12-34(40)41)29(36-27)15-30-25(11-13-35(42)43)20(5)28(38-30)16-33-23(9-2)21(6)32(39(33)7)17-31(22)37-26/h14-17,36-38H,8-13H2,1-7H3,(H,40,41)(H,42,43)/b26-14?,27-14-,28-16?,29-15?,30-15?,31-17?,32-17?,33-16?
InChIKey 
VIEXPEPYGOTUBM-IGZCREMUSA-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
PF00762

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_03616.

PDB 8

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

Ligand PDB entry

ChEMBL 3

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)