Ligand profile

ZM4

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

Bound to: KP13_01960 — Dihydrofolate reductase

Via homolog PDB 7mqp UniProt P0ABQ4 Formula C₂₄H₂₅N₅O
Mol. weight 399.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZM4
PDB
7mqp
UniProt (similar protein)
P0ABQ4
Target protein
KP13_01960

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 399.50 Da
LogP (Crippen) 3.43
H-bond donors 3
H-bond acceptors 5
TPSA 120.91 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 30
Fraction sp³ C 0.21
Formula C₂₄H₂₅N₅O

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 120.9
  • −1 ≤ LogP ≤ 5 3.43
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 399.5
  • LogP ≤ 5 3.43
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 120.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCc1c(c(nc(n1)N)N)C#CC(C)c2cc(ccc2C)c3ccc(cc3)C(=O)N
InChI 
InChI=1S/C24H25N5O/c1-4-21-19(22(25)29-24(27)28-21)12-6-15(3)20-13-18(7-5-14(20)2)16-8-10-17(11-9-16)23(26)30/h5,7-11,13,15H,4H2,1-3H3,(H2,26,30)(H4,25,27,28,29)
InChIKey 
YJUMTSDIAPDMCM-UHFFFAOYSA-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)