Ligand profile

NKD

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

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

Via homolog PDB 6oz6 UniProt O66465 Formula C₃₈H₄₈N₈O₁₃S
Mol. weight 856.91 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NKD
PDB
6oz6
UniProt (similar protein)
O66465
Target protein
VK055_2481

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 856.91 Da
LogP (Crippen) -1.83
H-bond donors 11
H-bond acceptors 15
TPSA 327.97 Ų
Rotatable bonds 18
Aromatic rings 3 / 4
Heavy atoms 60
Fraction sp³ C 0.39
Formula C₃₈H₄₈N₈O₁₃S

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 328.0
  • −1 ≤ LogP ≤ 5 -1.83
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 856.9
  • LogP ≤ 5 -1.83
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 18
  • TPSA ≤ 140 Ų 328.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]([C@@H](C(=O)N/C=C\1/[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)O)NC(=O)[C@H](CCSC)NC(=O)N[C@@H](Cc3cccc(c3)O)C(=O)O)N(C)C(=O)[C@H](Cc4cccc(c4)O)N
InChI 
InChI=1S/C38H48N8O13S/c1-19(45(2)34(54)24(39)16-20-6-4-8-22(47)14-20)29(33(53)40-18-27-30(50)31(51)35(59-27)46-12-10-28(49)43-38(46)58)44-32(52)25(11-13-60-3)41-37(57)42-26(36(55)56)17-21-7-5-9-23(48)15-21/h4-10,12,14-15,18-19,24-26,29-31,35,47-48,50-51H,11,13,16-17,39H2,1-3H3,(H,40,53)(H,44,52)(H,55,56)(H2,41,42,57)(H,43,49,58)/b27-18-/t19-,24-,25-,26-,29-,30+,31+,35+/m0/s1
InChIKey 
FPCKAOGINMZAIN-MNATZBQSSA-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)