Ligand profile

2NE

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

Bound to: VK055_4855 — naphthoate synthase

Via homolog PDB 4i4z UniProt P73495 Formula C₂₈H₄₀N₇O₁₈P₃S
Mol. weight 887.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2NE
PDB
4i4z
UniProt (similar protein)
P73495
Target protein
VK055_4855

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 887.65 Da
LogP (Crippen) -0.32
H-bond donors 10
H-bond acceptors 20
TPSA 383.86 Ų
Rotatable bonds 20
Aromatic rings 3 / 4
Heavy atoms 57
Fraction sp³ C 0.50
Formula C₂₈H₄₀N₇O₁₈P₃S

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 383.9
  • −1 ≤ LogP ≤ 5 -0.32
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 887.6
  • LogP ≤ 5 -0.32
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 383.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)c4ccccc4O)O
InChI 
InChI=1S/C28H40N7O18P3S/c1-28(2,22(39)25(40)31-8-7-18(37)30-9-10-57-27(41)15-5-3-4-6-16(15)36)12-50-56(47,48)53-55(45,46)49-11-17-21(52-54(42,43)44)20(38)26(51-17)35-14-34-19-23(29)32-13-33-24(19)35/h3-6,13-14,17,20-22,26,36,38-39H,7-12H2,1-2H3,(H,30,37)(H,31,40)(H,45,46)(H,47,48)(H2,29,32,33)(H2,42,43,44)/t17-,20-,21-,22+,26-/m1/s1
InChIKey 
YTKKDFTVSNSVEE-TYHXJLICSA-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
PF00378

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_4855.

PDB 11

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

Ligand PDB entry

ChEMBL 10

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)