Ligand profile

URD

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

Bound to: VK055_4939 — cytidine deaminase

Via homolog PDB 1zab UniProt P56389 Formula C₁₀H₁₃NO₆
Mol. weight 243.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
URD
PDB
1zab
UniProt (similar protein)
P56389
Target protein
VK055_4939

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 243.22 Da
LogP (Crippen) -2.26
H-bond donors 3
H-bond acceptors 6
TPSA 107.30 Ų
Rotatable bonds 2
Aromatic rings 0 / 2
Heavy atoms 17
Fraction sp³ C 0.60
Formula C₁₀H₁₃NO₆

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 107.3
  • −1 ≤ LogP ≤ 5 -2.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 243.2
  • LogP ≤ 5 -2.26
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 107.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
InChI 
InChI=1S/C10H13NO6/c12-4-6-8(15)9(16)10(17-6)11-2-1-5(13)3-7(11)14/h1-2,6,8-10,12,15-16H,3-4H2/t6-,8-,9-,10-/m1/s1
InChIKey 
WIRVQQCUKDPURA-PEBGCTIMSA-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
PF00383

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_4939.

PDB 8

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

Ligand PDB entry

ChEMBL 16

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)