Ligand profile

UMA

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

Bound to: VK055_2476 — UDP-N-acetylmuramate--alanine ligase

Via homolog PDB 1p3d UniProt P45066 Formula C₂₃H₃₆N₄O₂₀P₂
Mol. weight 750.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
UMA
PDB
1p3d
UniProt (similar protein)
P45066
Target protein
VK055_2476

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 750.50 Da
LogP (Crippen) -4.65
H-bond donors 10
H-bond acceptors 18
TPSA 361.26 Ų
Rotatable bonds 15
Aromatic rings 1 / 3
Heavy atoms 49
Fraction sp³ C 0.70
Formula C₂₃H₃₆N₄O₂₀P₂

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 361.3
  • −1 ≤ LogP ≤ 5 -4.65
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 750.5
  • LogP ≤ 5 -4.65
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 361.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](C(=O)O)NC(=O)[C@@H](C)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C
InChI 
InChI=1S/C23H36N4O20P2/c1-8(21(35)36)24-19(34)9(2)43-18-14(25-10(3)29)22(45-11(6-28)16(18)32)46-49(40,41)47-48(38,39)42-7-12-15(31)17(33)20(44-12)27-5-4-13(30)26-23(27)37/h4-5,8-9,11-12,14-18,20,22,28,31-33H,6-7H2,1-3H3,(H,24,34)(H,25,29)(H,35,36)(H,38,39)(H,40,41)(H,26,30,37)/t8-,9+,11+,12+,14+,15+,16+,17+,18+,20+,22+/m0/s1
InChIKey 
NTMMCWJNQNKACG-KBKUWGQMSA-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
PF01225' 'PF02875' 'PF08245

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_2476.

PDB 17

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)