Ligand profile

6ME

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

Bound to: KP13_01960 — Dihydrofolate reductase

Via homolog PDB 3r33 UniProt P0ABQ4 Formula C₉H₁₄N₄
Mol. weight 178.24 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6ME
PDB
3r33
UniProt (similar protein)
P0ABQ4
Target protein
KP13_01960

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 178.24 Da
LogP (Crippen) 0.77
H-bond donors 2
H-bond acceptors 4
TPSA 77.82 Ų
Rotatable bonds 0
Aromatic rings 1 / 2
Heavy atoms 13
Fraction sp³ C 0.56
Formula C₉H₁₄N₄

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 77.8
  • −1 ≤ LogP ≤ 5 0.77
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 178.2
  • LogP ≤ 5 0.77
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 77.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1CCc2c(c(nc(n2)N)N)C1
InChI 
InChI=1S/C9H14N4/c1-5-2-3-7-6(4-5)8(10)13-9(11)12-7/h5H,2-4H2,1H3,(H4,10,11,12,13)/t5-/m0/s1
InChIKey 
NQHPYDRZSXDOSD-YFKPBYRVSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00186

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_01960.

PDB 33

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

Ligand PDB entry

ChEMBL 100

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)