Ligand profile

GCP

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

Bound to: VK055_3750 — translation elongation factor Tu

Via homolog PDB 5uyk UniProt P0CE47 Formula C₁₁H₁₈N₅O₁₃P₃
Mol. weight 521.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GCP
PDB
5uyk
UniProt (similar protein)
P0CE47
Target protein
VK055_3750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 521.21 Da
LogP (Crippen) -2.22
H-bond donors 8
H-bond acceptors 13
TPSA 289.87 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.55
Formula C₁₁H₁₈N₅O₁₃P₃

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 289.9
  • −1 ≤ LogP ≤ 5 -2.22
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 521.2
  • LogP ≤ 5 -2.22
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 289.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(CP(=O)(O)O)O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C11H18N5O13P3/c12-11-14-8-5(9(19)15-11)13-2-16(8)10-7(18)6(17)4(28-10)1-27-32(25,26)29-31(23,24)3-30(20,21)22/h2,4,6-7,10,17-18H,1,3H2,(H,23,24)(H,25,26)(H2,20,21,22)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1
InChIKey 
PHBDHXOBFUBCJD-KQYNXXCUSA-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
PF00009

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3750.

PDB 19

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)