Ligand profile

KIR

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

Bound to: VK055_3750 — translation elongation factor Tu

Via homolog PDB 5afi UniProt P0CE48 Formula C₄₃H₆₀N₂O₁₂
Mol. weight 796.96 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KIR
PDB
5afi
UniProt (similar protein)
P0CE48
Target protein
VK055_3750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 796.96 Da
LogP (Crippen) 3.07
H-bond donors 8
H-bond acceptors 12
TPSA 228.10 Ų
Rotatable bonds 17
Aromatic rings 1 / 3
Heavy atoms 57
Fraction sp³ C 0.51
Formula C₄₃H₆₀N₂O₁₂

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 228.1
  • −1 ≤ LogP ≤ 5 3.07
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 797.0
  • LogP ≤ 5 3.07
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 17
  • TPSA ≤ 140 Ų 228.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@H](C(=O)NC\C=C\C=C(/C)\[C@H]([C@@H](C)[C@H]1[C@H]([C@H]([C@H](O1)\C=C\C=C\C=C(/C)\C(=O)C2=C(C=CNC2=O)O)O)O)OC)[C@@]3([C@@H]([C@@H](C([C@@H](O3)\C=C\C=C/C)(C)C)O)O)O
InChI 
InChI=1S/C43H60N2O12/c1-9-11-13-21-31-42(6,7)38(50)39(51)43(54,57-31)28(10-2)40(52)44-23-17-16-19-26(4)36(55-8)27(5)37-35(49)34(48)30(56-37)20-15-12-14-18-25(3)33(47)32-29(46)22-24-45-41(32)53/h9,11-22,24,27-28,30-31,34-39,48-51,54H,10,23H2,1-8H3,(H,44,52)(H2,45,46,53)/b11-9-,14-12+,17-16+,20-15+,21-13+,25-18+,26-19+/t27-,28-,30-,31+,34+,35+,36-,37+,38+,39-,43-/m1/s1
InChIKey 
HMSYAPGFKGSXAJ-PAHGNTJYSA-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' 'PF03143

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)