Ligand profile

SND

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

Bound to: KP13_32247 — Glyceraldehyde-3-phosphate dehydrogenase

Via homolog PDB 1ihx UniProt P56649 Formula C₂₁H₂₇N₇O₁₃P₂S
Mol. weight 679.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SND
PDB
1ihx
UniProt (similar protein)
P56649
Target protein
KP13_32247

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 679.50 Da
LogP (Crippen) -3.11
H-bond donors 7
H-bond acceptors 18
TPSA 304.02 Ų
Rotatable bonds 11
Aromatic rings 3 / 5
Heavy atoms 44
Fraction sp³ C 0.48
Formula C₂₁H₂₇N₇O₁₃P₂S

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 304.0
  • −1 ≤ LogP ≤ 5 -3.11
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 679.5
  • LogP ≤ 5 -3.11
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 304.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=S)N
InChI 
InChI=1S/C21H27N7O13P2S/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(40-21)6-38-43(35,36)41-42(33,34)37-5-10-13(29)15(31)20(39-10)27-3-1-2-9(4-27)18(23)44/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,44)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKey 
UQYPZLRUJKCREN-NNYOXOHSSA-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
PF00044

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_32247.

PDB 7

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

Ligand PDB entry

ChEMBL 3

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)