Ligand profile

999

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

Bound to: VK055_2645 — putative D-serine deaminase (D-serine dehydratase) protein

Via homolog PDB 3wqd UniProt B2DFG5 Formula C₄H₇NO₅
Mol. weight 149.10 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
999
PDB
3wqd
UniProt (similar protein)
B2DFG5
Target protein
VK055_2645

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 149.10 Da
LogP (Crippen) -2.16
H-bond donors 4
H-bond acceptors 4
TPSA 120.85 Ų
Rotatable bonds 3
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 0.50
Formula C₄H₇NO₅

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 120.8
  • −1 ≤ LogP ≤ 5 -2.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 149.1
  • LogP ≤ 5 -2.16
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 120.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[C@@H]([C@@H](C(=O)O)O)(C(=O)O)N
InChI 
InChI=1S/C4H7NO5/c5-1(3(7)8)2(6)4(9)10/h1-2,6H,5H2,(H,7,8)(H,9,10)/t1-,2+/m1/s1
InChIKey 
YYLQUHNPNCGKJQ-NCGGTJAESA-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
PF01168' 'PF14031

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_2645.

PDB 1

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

Ligand PDB entry

ZINC 14

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)