Binder profile

UML

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

Bound to: PA4416 — UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase

Via homolog PDB 4c12 UniProt Q2FZP6 C34H55N7O24P2
Mol. weight 1007.79 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
UML
PDB
4c12
UniProt (similar protein)
Q2FZP6
Target protein
PA4416

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1007.79 Da
LogP (Crippen) -5.68
H-bond donors 14
H-bond acceptors 22
TPSA 482.78 Ų
Rotatable bonds 26
Aromatic rings 1 / 3
Heavy atoms 67
Fraction sp³ C 0.71
Formula C34H55N7O24P2

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.

Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1007.8
  • LogP ≤ 5 -5.68
  • H-bond donors ≤ 5 14
  • H-bond acceptors ≤ 10 22
Veber's rules Fail
  • Rotatable bonds ≤ 10 26
  • TPSA ≤ 140 Ų 482.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCCCN)C(=O)O)C(=O)O)NC(=O)[C@@H](C)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)OP(=O)(O)OP(=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/C34H55N7O24P2/c1-14(28(49)39-18(32(53)54)7-8-21(44)38-17(31(51)52)6-4-5-10-35)36-29(50)15(2)61-27-23(37-16(3)43)33(63-19(12-42)25(27)47)64-67(58,59)65-66(56,57)60-13-20-24(46)26(48)30(62-20)41-11-9-22(45)40-34(41)55/h9,11,14-15,17-20,23-27,30,33,42,46-48H,4-8,10,12-13,35H2,1-3H3,(H,36,50)(H,37,43)(H,38,44)(H,39,49)(H,51,52)(H,53,54)(H,56,57)(H,58,59)(H,40,45,55)/t14-,15+,17-,18+,19+,20+,23+,24+,25+,26+,27+,30+,33+/m0/s1
InChIKey 
WXBLSQNZKMJACT-BYEZXYKXSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF02875' 'PF08245

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA4416.

PDB 8

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

Ligand PDB entry

ChEMBL 9

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)