Ligand profile

9G1

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

Bound to: VK055_4541 — short chain dehydrogenase family protein

Via homolog PDB 5vps UniProt B1YU47 Formula C₃₀H₄₈N₇O₂₃P₄⁺
Mol. weight 998.64 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9G1
PDB
5vps
UniProt (similar protein)
B1YU47
Target protein
VK055_4541

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 998.64 Da
LogP (Crippen) -2.54
H-bond donors 12
H-bond acceptors 22
TPSA 476.05 Ų
Rotatable bonds 23
Aromatic rings 2 / 5
Heavy atoms 64
Fraction sp³ C 0.70
Formula C₃₀H₄₈N₇O₂₃P₄⁺

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 476.1
  • −1 ≤ LogP ≤ 5 -2.54
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 998.6
  • LogP ≤ 5 -2.54
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 22
Veber's rules Fail
  • Rotatable bonds ≤ 10 23
  • TPSA ≤ 140 Ų 476.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5CC[C@@H](C(C5)C(=O)N)[P+](CCC(=O)O)(CCC(=O)O)CCC(=O)O)O)O)O)OP(=O)(O)O)N
InChI 
InChI=1S/C30H47N7O23P4/c31-26-21-28(34-12-33-26)37(13-35-21)30-25(59-62(48,49)50)23(45)16(58-30)11-56-64(53,54)60-63(51,52)55-10-15-22(44)24(46)29(57-15)36-5-1-17(14(9-36)27(32)47)61(6-2-18(38)39,7-3-19(40)41)8-4-20(42)43/h12-17,22-25,29-30,44-46H,1-11H2,(H10-,31,32,33,34,38,39,40,41,42,43,47,48,49,50,51,52,53,54)/p+1/t14?,15-,16-,17+,22-,23-,24-,25-,29-,30-/m1/s1
InChIKey 
KCEMQRAWVXDPSM-UWRGCXDJSA-O

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
PF13561

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_4541.

PDB 5

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)