Ligand profile

CMK

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

Bound to: VK055_1539 — 3-deoxy-D-manno-octulosonate cytidylyltransferase

Via homolog PDB 1vh3 UniProt P44490 Formula C₁₇H₂₆N₃O₁₅P
Mol. weight 543.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CMK
PDB
1vh3
UniProt (similar protein)
P44490
Target protein
VK055_1539

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 543.38 Da
LogP (Crippen) -4.78
H-bond donors 9
H-bond acceptors 16
TPSA 293.81 Ų
Rotatable bonds 9
Aromatic rings 1 / 3
Heavy atoms 36
Fraction sp³ C 0.71
Formula C₁₇H₂₆N₃O₁₅P

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 293.8
  • −1 ≤ LogP ≤ 5 -4.78
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 543.4
  • LogP ≤ 5 -4.78
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 293.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@H]([C@H]([C@H](O[C@@]1(C(=O)O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)[C@@H](CO)O)O)O
InChI 
InChI=1S/C17H26N3O15P/c18-9-1-2-20(16(29)19-9)14-12(26)11(25)8(33-14)5-32-36(30,31)35-17(15(27)28)3-6(22)10(24)13(34-17)7(23)4-21/h1-2,6-8,10-14,21-26H,3-5H2,(H,27,28)(H,30,31)(H2,18,19,29)/t6-,7-,8-,10-,11-,12-,13-,14-,17-/m1/s1
InChIKey 
YWWJKULNWGRYAS-UOVSKDHASA-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
PF02348

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_1539.

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)