Ligand profile

NAE

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

Bound to: VK055_0642 — short chain dehydrogenase family protein

Via homolog PDB 3i3o UniProt A0A6L8PL20 Formula C₂₄H₃₁N₇O₁₅P₂
Mol. weight 719.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NAE
PDB
3i3o
UniProt (similar protein)
A0A6L8PL20
Target protein
VK055_0642

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 719.49 Da
LogP (Crippen) -3.52
H-bond donors 7
H-bond acceptors 19
TPSA 338.16 Ų
Rotatable bonds 13
Aromatic rings 3 / 5
Heavy atoms 48
Fraction sp³ C 0.50
Formula C₂₄H₃₁N₇O₁₅P₂

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 338.2
  • −1 ≤ LogP ≤ 5 -3.52
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 719.5
  • LogP ≤ 5 -3.52
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 338.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)Cc1cc[n+](cc1C(=O)N)[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)n4cnc5c4ncnc5N)O)O)O)O
InChI 
InChI=1S/C24H31N7O15P2/c1-10(32)4-11-2-3-30(5-12(11)21(26)37)23-18(35)16(33)13(44-23)6-42-47(38,39)46-48(40,41)43-7-14-17(34)19(36)24(45-14)31-9-29-15-20(25)27-8-28-22(15)31/h2-3,5,8-9,13-14,16-19,23-24,33-36H,4,6-7H2,1H3,(H5-,25,26,27,28,37,38,39,40,41)/t13-,14-,16-,17-,18-,19-,23-,24-/m1/s1
InChIKey 
SGHBFOOIAAJJMI-YDKVLQLQSA-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
PF13561

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_0642.

PDB 11

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

Ligand PDB entry

ChEMBL 1

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)