Ligand profile

NDO

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

Bound to: VK055_1318 — isocitrate dehydrogenase, NADP-dependent

Via homolog PDB 1ai3 UniProt P08200 Formula C₂₁H₂₇N₆O₁₈P₃
Mol. weight 744.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NDO
PDB
1ai3
UniProt (similar protein)
P08200
Target protein
VK055_1318

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 744.39 Da
LogP (Crippen) -3.41
H-bond donors 8
H-bond acceptors 19
TPSA 361.83 Ų
Rotatable bonds 13
Aromatic rings 3 / 5
Heavy atoms 48
Fraction sp³ C 0.48
Formula C₂₁H₂₇N₆O₁₈P₃

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 361.8
  • −1 ≤ LogP ≤ 5 -3.41
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 744.4
  • LogP ≤ 5 -3.41
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 361.8
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)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5O)OP(=O)(O)O)O)O)O)C(=O)N
InChI 
InChI=1S/C21H27N6O18P3/c22-17(31)9-2-1-3-26(4-9)20-15(30)13(28)10(42-20)5-40-47(36,37)45-48(38,39)41-6-11-14(29)16(44-46(33,34)35)21(43-11)27-8-25-12-18(27)23-7-24-19(12)32/h1-4,7-8,10-11,13-16,20-21,28-30H,5-6H2,(H6-,22,23,24,31,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKey 
WKSUSMNNBQFESD-NNYOXOHSSA-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
PF00180

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_1318.

PDB 10

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)