Ligand profile

HMT

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

Bound to: KP13_02169 — D-3-phosphoglycerate dehydrogenase

Via homolog PDB 7ewh UniProt O43175 Formula C₂₉H₃₉NO₉
Mol. weight 545.63 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HMT
PDB
7ewh
UniProt (similar protein)
O43175
Target protein
KP13_02169

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 545.63 Da
LogP (Crippen) 2.58
H-bond donors 2
H-bond acceptors 10
TPSA 123.99 Ų
Rotatable bonds 9
Aromatic rings 1 / 5
Heavy atoms 39
Fraction sp³ C 0.66
Formula C₂₉H₃₉NO₉

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 124.0
  • −1 ≤ LogP ≤ 5 2.58
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 545.6
  • LogP ≤ 5 2.58
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 10
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 124.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CCC[C@@](CC(=O)OC)(C(=O)O[C@H]1[C@H]2c3cc4c(cc3CC[N@@]5[C@@]2(CCC5)C=C1OC)OCO4)O)O
InChI 
InChI=1S/C29H39NO9/c1-27(2,33)8-5-10-29(34,16-23(31)36-4)26(32)39-25-22(35-3)15-28-9-6-11-30(28)12-7-18-13-20-21(38-17-37-20)14-19(18)24(25)28/h13-15,24-25,33-34H,5-12,16-17H2,1-4H3/t24-,25-,28+,29-/m1/s1
InChIKey 
HYFHYPWGAURHIV-JFIAXGOJSA-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
PF00389' 'PF02826

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_02169.

PDB 19

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)