Ligand profile

3X4

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

Bound to: KP13_00958 — Ribonucleoside-diphosphate reductase 1 subunit alpha

Via homolog PDB 4x3v UniProt P23921 Formula C₂₀H₂₆N₄O₆
Mol. weight 418.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3X4
PDB
4x3v
UniProt (similar protein)
P23921
Target protein
KP13_00958

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 418.45 Da
LogP (Crippen) -0.12
H-bond donors 4
H-bond acceptors 6
TPSA 158.90 Ų
Rotatable bonds 10
Aromatic rings 1 / 2
Heavy atoms 30
Fraction sp³ C 0.45
Formula C₂₀H₂₆N₄O₆

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 158.9
  • −1 ≤ LogP ≤ 5 -0.12
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 418.5
  • LogP ≤ 5 -0.12
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 158.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C(=O)NCCCC[C@H](C(=O)O)N)NC(=O)CN1C(=O)c2ccccc2C1=O
InChI 
InChI=1S/C20H26N4O6/c1-20(2,19(30)22-10-6-5-9-14(21)18(28)29)23-15(25)11-24-16(26)12-7-3-4-8-13(12)17(24)27/h3-4,7-8,14H,5-6,9-11,21H2,1-2H3,(H,22,30)(H,23,25)(H,28,29)/t14-/m1/s1
InChIKey 
HSKHXKLBWCBTSW-CQSZACIVSA-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
PF02867

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00958.

PDB 15

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

Ligand PDB entry

ChEMBL 9

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)