Ligand profile

MMP

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

Bound to: KP13_03616 — Ferrochelatase

Via homolog PDB 1c1h UniProt P32396 Formula C₃₅H₄₀N₄O₄
Mol. weight 580.73 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MMP
PDB
1c1h
UniProt (similar protein)
P32396
Target protein
KP13_03616

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 580.73 Da
LogP (Crippen) 7.66
H-bond donors 3
H-bond acceptors 5
TPSA 121.10 Ų
Rotatable bonds 8
Aromatic rings 3 / 5
Heavy atoms 43
Fraction sp³ C 0.37
Formula C₃₅H₄₀N₄O₄

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 121.1
  • −1 ≤ LogP ≤ 5 7.66
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 580.7
  • LogP ≤ 5 7.66
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 121.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCc1c(c2cc3nc(\cc/4\c(c(/c(/[nH]4)c/c5n/c(c\c1n2C)/C(=C5CC)C)C)CCC(=O)O)C(=C3C)CCC(=O)O)C
InChI 
InChI=1S/C35H40N4O4/c1-8-22-18(3)28-17-33-23(9-2)21(6)32(39(33)7)16-27-20(5)25(11-13-35(42)43)31(38-27)15-30-24(10-12-34(40)41)19(4)26(36-30)14-29(22)37-28/h14-17,36H,8-13H2,1-7H3,(H,40,41)(H,42,43)
InChIKey 
YNWHQWMCLCANDI-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
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)