Ligand profile

ZP1

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

Bound to: KP13_03277 — 2-oxoglutarate dehydrogenase E1 component

Via homolog PDB 6r2a UniProt A0R2B1 Formula C₁₈H₃₁N₄O₁₃P₃S
Mol. weight 636.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZP1
PDB
6r2a
UniProt (similar protein)
A0R2B1
Target protein
KP13_03277

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 636.45 Da
LogP (Crippen) 1.87
H-bond donors 7
H-bond acceptors 13
TPSA 272.39 Ų
Rotatable bonds 15
Aromatic rings 1 / 2
Heavy atoms 39
Fraction sp³ C 0.61
Formula C₁₈H₃₁N₄O₁₃P₃S

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 272.4
  • −1 ≤ LogP ≤ 5 1.87
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 636.5
  • LogP ≤ 5 1.87
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 272.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCOP(=O)([C@@](CCC(=O)O)([C@@H]1N(C(=C(S1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)O)O
InChI 
InChI=1S/C18H31N4O13P3S/c1-4-33-36(26,27)18(25,7-5-15(23)24)17-22(10-13-9-20-12(3)21-16(13)19)11(2)14(39-17)6-8-34-38(31,32)35-37(28,29)30/h9,17,25H,4-8,10H2,1-3H3,(H,23,24)(H,26,27)(H,31,32)(H2,19,20,21)(H2,28,29,30)/t17-,18+/m1/s1
InChIKey 
XUQXUYTXDQCESE-MSOLQXFVSA-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
PF00676' 'PF02779

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_03277.

PDB 9

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)