Ligand profile

6MP

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

Bound to: KP13_00003 — Ribose operon repressor

Via homolog PDB 2pua UniProt P0ACP7 Formula C₆H₆N₄
Mol. weight 134.14 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6MP
PDB
2pua
UniProt (similar protein)
P0ACP7
Target protein
KP13_00003

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 134.14 Da
LogP (Crippen) 0.66
H-bond donors 1
H-bond acceptors 3
TPSA 54.46 Ų
Rotatable bonds 0
Aromatic rings 2 / 2
Heavy atoms 10
Fraction sp³ C 0.17
Formula C₆H₆N₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 54.5
  • −1 ≤ LogP ≤ 5 0.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 134.1
  • LogP ≤ 5 0.66
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 54.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c2c(nc[nH]2)ncn1
InChI 
InChI=1S/C6H6N4/c1-4-5-6(9-2-7-4)10-3-8-5/h2-3H,1H3,(H,7,8,9,10)
InChIKey 
SYMHUEFSSMBHJA-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
PF13377

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_00003.

PDB 5

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

Ligand PDB entry

ZINC 37

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

Compound Similarity (Tanimoto)