Ligand profile

7MD

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

Bound to: KP13_05059 — putative murein peptide carboxypeptidase

Via homolog PDB 3tlc UniProt Q47511 Formula C₁₇H₂₇N₈O₉P
Mol. weight 518.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7MD
PDB
3tlc
UniProt (similar protein)
Q47511
Target protein
KP13_05059

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 518.42 Da
LogP (Crippen) -2.56
H-bond donors 7
H-bond acceptors 15
TPSA 273.28 Ų
Rotatable bonds 12
Aromatic rings 2 / 3
Heavy atoms 35
Fraction sp³ C 0.59
Formula C₁₇H₂₇N₈O₉P

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 273.3
  • −1 ≤ LogP ≤ 5 -2.56
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 518.4
  • LogP ≤ 5 -2.56
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 273.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(NC(=O)[C@H](CC(=O)O)N)OCCCN)O)O)N
InChI 
InChI=1S/C17H27N8O9P/c18-2-1-3-32-35(31,24-16(30)8(19)4-10(26)27)33-5-9-12(28)13(29)17(34-9)25-7-23-11-14(20)21-6-22-15(11)25/h6-9,12-13,17,28-29H,1-5,18-19H2,(H,26,27)(H2,20,21,22)(H,24,30,31)/t8-,9+,12+,13+,17+,35+/m0/s1
InChIKey 
CBRVFFLBHDTTIM-FGNORGMNSA-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
PF02016' 'PF17676

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_05059.

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)