Ligand profile

MW5

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

Bound to: KP13_02514 — 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

Via homolog PDB 2yc3 UniProt P69834 Formula C₁₂H₉ClN₄O
Mol. weight 260.68 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MW5
PDB
2yc3
UniProt (similar protein)
P69834
Target protein
KP13_02514

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 260.68 Da
LogP (Crippen) 1.66
H-bond donors 1
H-bond acceptors 4
TPSA 63.05 Ų
Rotatable bonds 2
Aromatic rings 3 / 3
Heavy atoms 18
Fraction sp³ C 0.08
Formula C₁₂H₉ClN₄O

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 63.1
  • −1 ≤ LogP ≤ 5 1.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 260.7
  • LogP ≤ 5 1.66
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 63.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)CC2=C(N=C3NC=NN3C2=O)Cl
InChI 
InChI=1S/C12H9ClN4O/c13-10-9(6-8-4-2-1-3-5-8)11(18)17-12(16-10)14-7-15-17/h1-5,7H,6H2,(H,14,15,16)
InChIKey 
MQEBPOLOTAZMKF-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
PF01128

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_02514.

PDB 6

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

Ligand PDB entry

ChEMBL 6

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)