Binder profile

D4X

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

Bound to: PA3700 — lysine--tRNA ligase

Via homolog PDB 6kbf UniProt W7JP72 C17H23NO3
Mol. weight 289.38 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D4X
PDB
6kbf
UniProt (similar protein)
W7JP72
Target protein
PA3700

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 289.38 Da
LogP (Crippen) 2.97
H-bond donors 3
H-bond acceptors 3
TPSA 69.56 Ų
Rotatable bonds 2
Aromatic rings 1 / 3
Heavy atoms 21
Fraction sp³ C 0.59
Formula C17H23NO3

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 Pass 0 violations
  • MW ≤ 500 Da 289.4
  • LogP ≤ 5 2.97
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 69.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1CCC[C@@H](C1)C[C@H]2Cc3cc(cc(c3C(=O)N2)O)O
InChI 
InChI=1S/C17H23NO3/c1-10-3-2-4-11(5-10)6-13-7-12-8-14(19)9-15(20)16(12)17(21)18-13/h8-11,13,19-20H,2-7H2,1H3,(H,18,21)/t10-,11-,13-/m0/s1
InChIKey 
YKYWGEWGZHSEGR-GVXVVHGQSA-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
PF00152

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3700.

PDB 16

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

Ligand PDB entry

ChEMBL 2

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)