Ligand profile

3YB

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

Bound to: KP13_03811 — Phosphoribosylglycinamide formyltransferase

Via homolog PDB 4zyx UniProt P22102 Formula C₂₀H₂₃N₅O₆S
Mol. weight 461.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3YB
PDB
4zyx
UniProt (similar protein)
P22102
Target protein
KP13_03811

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 461.50 Da
LogP (Crippen) 1.51
H-bond donors 6
H-bond acceptors 7
TPSA 191.26 Ų
Rotatable bonds 11
Aromatic rings 3 / 3
Heavy atoms 32
Fraction sp³ C 0.35
Formula C₂₀H₂₃N₅O₆S

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 191.3
  • −1 ≤ LogP ≤ 5 1.51
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 461.5
  • LogP ≤ 5 1.51
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 191.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(csc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)CCCCc2cc3c([nH]2)N=C(NC3=O)N
InChI 
InChI=1S/C20H23N5O6S/c21-20-24-16-12(17(28)25-20)8-11(22-16)4-2-1-3-10-7-14(32-9-10)18(29)23-13(19(30)31)5-6-15(26)27/h7-9,13H,1-6H2,(H,23,29)(H,26,27)(H,30,31)(H4,21,22,24,25,28)/t13-/m0/s1
InChIKey 
VMGGIKVXYOZFJO-ZDUSSCGKSA-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
PF00551

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_03811.

PDB 22

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

Ligand PDB entry

ChEMBL 74

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)