Ligand profile

UML

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

Bound to: KP13_31828 — UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase

Via homolog PDB 4c12 UniProt Q2FZP6 Formula 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
KP13_31828

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.

  • TPSA ≤ 90 Ų 482.8
  • −1 ≤ LogP ≤ 5 -5.68
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 Target 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 ligands for this protein

Quick navigation to other ligands bound to KP13_31828.

PDB 17

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)