Ligand profile

7J8

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

Bound to: KP13_01706 — Porphobilinogen deaminase

Via homolog PDB 5m6r UniProt P08397 Formula C₄₀H₄₆N₄O₁₆
Mol. weight 838.82 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7J8
PDB
5m6r
UniProt (similar protein)
P08397
Target protein
KP13_01706

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 838.82 Da
LogP (Crippen) 2.66
H-bond donors 12
H-bond acceptors 8
TPSA 361.56 Ų
Rotatable bonds 26
Aromatic rings 4 / 4
Heavy atoms 60
Fraction sp³ C 0.40
Formula C₄₀H₄₆N₄O₁₆

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 361.6
  • −1 ≤ LogP ≤ 5 2.66
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 838.8
  • LogP ≤ 5 2.66
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 26
  • TPSA ≤ 140 Ų 361.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c([nH]1)Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc4c(c(c[nH]4)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
InChI 
InChI=1S/C40H46N4O16/c1-18-23(10-37(53)54)20(3-7-34(47)48)28(42-18)15-31-26(13-40(59)60)22(5-9-36(51)52)30(44-31)16-32-25(12-39(57)58)21(4-8-35(49)50)29(43-32)14-27-24(11-38(55)56)19(17-41-27)2-6-33(45)46/h17,41-44H,2-16H2,1H3,(H,45,46)(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)
InChIKey 
VHZWMEJYGVBAFI-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
PF01379' 'PF03900

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_01706.

PDB 5

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

Ligand PDB entry

ZINC 1

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)