Ligand profile

WMP

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

Bound to: HT085_RS00030 — leucine--tRNA ligase

Via homolog PDB 4k47 UniProt B8ZKS5 Formula C₂₄H₂₄BN₅O₉P⁻
Mol. weight 568.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
WMP
PDB
4k47
UniProt (similar protein)
B8ZKS5
Target protein
HT085_RS00030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 568.27 Da
LogP (Crippen) 0.66
H-bond donors 4
H-bond acceptors 12
TPSA 193.53 Ų
Rotatable bonds 6
Aromatic rings 4 / 7
Heavy atoms 40
Fraction sp³ C 0.29
Formula C₂₄H₂₄BN₅O₉P⁻

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 193.5
  • −1 ≤ LogP ≤ 5 0.66
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 568.3
  • LogP ≤ 5 0.66
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 193.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[B-]12(c3cc(ccc3CO1)[C@@H](c4ccccc4)O)O[C@H]5[C@@H](O[C@H]([C@@H]5O2)n6cnc7c6ncnc7N)COP(=O)(O)O
InChI 
InChI=1S/C24H24BN5O9P/c26-22-18-23(28-11-27-22)30(12-29-18)24-21-20(17(37-24)10-36-40(32,33)34)38-25(39-21)16-8-14(6-7-15(16)9-35-25)19(31)13-4-2-1-3-5-13/h1-8,11-12,17,19-21,24,31H,9-10H2,(H2,26,27,28)(H2,32,33,34)/q-1/t17-,19+,20-,21+,24+,25?/m0/s1
InChIKey 
XRLFSRQDERUGQF-DKUXFTKGSA-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
PF13603

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to HT085_RS00030.

PDB 20

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

Ligand PDB entry

ChEMBL 21

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)