Ligand profile

GV6

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

Bound to: KP13_31833 — Isoleucyl-tRNA synthetase

Via homolog PDB 7d5c UniProt P09436 Formula C₁₆H₂₅N₆O₈P
Mol. weight 460.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GV6
PDB
7d5c
UniProt (similar protein)
P09436
Target protein
KP13_31833

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 460.38 Da
LogP (Crippen) -0.94
H-bond donors 5
H-bond acceptors 13
TPSA 218.16 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.62
Formula C₁₆H₂₅N₆O₈P

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 218.2
  • −1 ≤ LogP ≤ 5 -0.94
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 460.4
  • LogP ≤ 5 -0.94
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 218.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@H](C)[C@@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
InChI 
InChI=1S/C16H25N6O8P/c1-3-7(2)9(17)16(25)30-31(26,27)28-4-8-11(23)12(24)15(29-8)22-6-21-10-13(18)19-5-20-14(10)22/h5-9,11-12,15,23-24H,3-4,17H2,1-2H3,(H,26,27)(H2,18,19,20)/t7-,8+,9-,11+,12+,15+/m0/s1
InChIKey 
ACZWYNUJBRLCEC-XATJSACLSA-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
PF00133

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_31833.

PDB 2

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

Ligand PDB entry

ChEMBL 34

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)