Ligand profile

3P7

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

Bound to: VK055_1079 — metallo-beta-lactamase superfamily protein

Via homolog PDB 6u2z UniProt B2FTM1 Formula C₁₈H₁₈N₂O₉
Mol. weight 406.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3P7
PDB
6u2z
UniProt (similar protein)
B2FTM1
Target protein
VK055_1079

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 406.35 Da
LogP (Crippen) -0.34
H-bond donors 4
H-bond acceptors 8
TPSA 171.82 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 29
Fraction sp³ C 0.28
Formula C₁₈H₁₈N₂O₉

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 171.8
  • −1 ≤ LogP ≤ 5 -0.34
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 406.3
  • LogP ≤ 5 -0.34
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 171.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CO[C@@](C=O)([C@@H]1N=C(C(=C)CO1)C(=O)O)NC(=O)[C@@H](c2ccc(cc2)O)C(=O)O
InChI 
InChI=1S/C18H18N2O9/c1-9-7-29-17(19-13(9)16(26)27)18(8-21,28-2)20-14(23)12(15(24)25)10-3-5-11(22)6-4-10/h3-6,8,12,17,22H,1,7H2,2H3,(H,20,23)(H,24,25)(H,26,27)/t12-,17-,18+/m1/s1
InChIKey 
GOYCBKVVHGALFQ-PJSAGSTRSA-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
PF00753

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_1079.

PDB 18

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

Ligand PDB entry

ChEMBL 37

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)