Ligand profile

6DD

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

Bound to: VK055_3785 — methionyl-tRNA formyltransferase

Via homolog PDB 4tts UniProt E3NZ06 Formula C₂₂H₂₁N₅O₇
Mol. weight 467.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6DD
PDB
4tts
UniProt (similar protein)
E3NZ06
Target protein
VK055_3785

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 467.44 Da
LogP (Crippen) 1.13
H-bond donors 5
H-bond acceptors 8
TPSA 196.04 Ų
Rotatable bonds 10
Aromatic rings 3 / 3
Heavy atoms 34
Fraction sp³ C 0.18
Formula C₂₂H₂₁N₅O₇

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 196.0
  • −1 ≤ LogP ≤ 5 1.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 467.4
  • LogP ≤ 5 1.13
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 196.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)N(Cc2ccc3c(c2)c(nc(n3)N)O)C=O
InChI 
InChI=1S/C22H21N5O7/c23-22-25-16-6-1-12(9-15(16)20(32)26-22)10-27(11-28)14-4-2-13(3-5-14)19(31)24-17(21(33)34)7-8-18(29)30/h1-6,9,11,17H,7-8,10H2,(H,24,31)(H,29,30)(H,33,34)(H3,23,25,26,32)/t17-/m0/s1
InChIKey 
QHUBQNFYSLRYQG-KRWDZBQOSA-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
PF00551

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_3785.

PDB 10

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)