Ligand profile

HAM

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

Bound to: KP13_00862 — Histidyl-tRNA synthetase

Via homolog PDB 1kmm UniProt P60906 Formula C₁₆H₂₁N₈O₈P
Mol. weight 484.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HAM
PDB
1kmm
UniProt (similar protein)
P60906
Target protein
KP13_00862

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 484.37 Da
LogP (Crippen) -3.37
H-bond donors 5
H-bond acceptors 14
TPSA 251.29 Ų
Rotatable bonds 8
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.44
Formula C₁₆H₂₁N₈O₈P

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 251.3
  • −1 ≤ LogP ≤ 5 -3.37
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 484.4
  • LogP ≤ 5 -3.37
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 251.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(nc[nH]1)C[C@@H](C(=O)O[P@](=O)([O-])OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)[NH3+]
InChI 
InChI=1S/C16H21N8O8P/c17-8(1-7-2-19-4-20-7)16(27)32-33(28,29)30-3-9-11(25)12(26)15(31-9)24-6-23-10-13(18)21-5-22-14(10)24/h2,4-6,8-9,11-12,15,25-26H,1,3,17H2,(H,19,20)(H,28,29)(H2,18,21,22)/t8-,9+,11+,12+,15+/m0/s1
InChIKey 
XTFBSLZFYLGYAT-OPYVMVOTSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00587

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_00862.

PDB 2

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)