Ligand profile

NK4

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

Bound to: VK055_2481 — phospho-N-acetylmuramoyl-pentapeptide- transferase

Via homolog PDB 6oyh UniProt O66465 Formula C₃₉H₆₇N₅O₁₂
Mol. weight 797.99 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NK4
PDB
6oyh
UniProt (similar protein)
O66465
Target protein
VK055_2481

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 797.99 Da
LogP (Crippen) 1.05
H-bond donors 7
H-bond acceptors 14
TPSA 250.34 Ų
Rotatable bonds 23
Aromatic rings 1 / 4
Heavy atoms 56
Fraction sp³ C 0.85
Formula C₃₉H₆₇N₅O₁₂

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 250.3
  • −1 ≤ LogP ≤ 5 1.05
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 798.0
  • LogP ≤ 5 1.05
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 23
  • TPSA ≤ 140 Ų 250.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCCC[C@H]1CN([C@H](C(=O)N([C@@H]1C(=O)O)C)[C@@H]([C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)O[C@H]4[C@@H]([C@@H]([C@H](O4)CN)O)O)C
InChI 
InChI=1S/C39H67N5O12/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-24-23-42(2)28(35(50)43(3)27(24)37(51)52)33(56-38-32(49)29(46)25(22-40)54-38)34-30(47)31(48)36(55-34)44-21-20-26(45)41-39(44)53/h20-21,24-25,27-34,36,38,46-49H,4-19,22-23,40H2,1-3H3,(H,51,52)(H,41,45,53)/t24-,25+,27-,28-,29+,30-,31+,32+,33-,34-,36+,38-/m0/s1
InChIKey 
GERCPLXZNIROKC-PUWYXTMPSA-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
PF00953' 'PF10555

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_2481.

PDB 1

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

Ligand PDB entry

ChEMBL 35

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)