Ligand profile

ZINC59207431

Virtual-screening candidate from ZINC.

Bound to: KP13_02981 — Malate dehydrogenase

Via homolog UniProt P61889 Formula C₁₄H₂₁N₆O₇P
Tanimoto 0.60
Mol. weight 416.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC59207431
UniProt (similar protein)
P61889
Tanimoto
0.600
Target protein
KP13_02981

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 416.33 Da
LogP (Crippen) -1.52
H-bond donors 4
H-bond acceptors 11
TPSA 178.31 Ų
Rotatable bonds 5
Aromatic rings 2 / 4
Heavy atoms 28
Fraction sp³ C 0.64
Formula C₁₄H₂₁N₆O₇P

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 178.3
  • −1 ≤ LogP ≤ 5 -1.52
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 416.3
  • LogP ≤ 5 -1.52
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 178.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)N2CCOCC2)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C14H21N6O7P/c15-12-9-13(17-6-16-12)20(7-18-9)14-11(22)10(21)8(27-14)5-26-28(23,24)19-1-3-25-4-2-19/h6-8,10-11,14,21-22H,1-5H2,(H,23,24)(H2,15,16,17)/t8-,10-,11-,14-/m1/s1
InChIKey 
XXDDQPLHHUHJOU-IDTAVKCVSA-N

Provenance

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

Method
LigQ sequence
Query
6V0
Homolog
P61889

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_02981.

PDB 4

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)