Ligand profile

DZF

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

Bound to: KP13_03811 — Phosphoribosylglycinamide formyltransferase

Via homolog PDB 1cde UniProt P08179 Formula C₂₀H₂₀N₆O₆
Mol. weight 440.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DZF
PDB
1cde
UniProt (similar protein)
P08179
Target protein
KP13_03811

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 440.42 Da
LogP (Crippen) 0.56
H-bond donors 6
H-bond acceptors 8
TPSA 200.39 Ų
Rotatable bonds 9
Aromatic rings 3 / 3
Heavy atoms 32
Fraction sp³ C 0.20
Formula C₂₀H₂₀N₆O₆

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 200.4
  • −1 ≤ LogP ≤ 5 0.56
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 440.4
  • LogP ≤ 5 0.56
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 200.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCc2cc3c(nc2)NC(=NC3=O)N
InChI 
InChI=1S/C20H20N6O6/c21-20-25-16-13(18(30)26-20)7-10(9-23-16)8-22-12-3-1-11(2-4-12)17(29)24-14(19(31)32)5-6-15(27)28/h1-4,7,9,14,22H,5-6,8H2,(H,24,29)(H,27,28)(H,31,32)(H3,21,23,25,26,30)/t14-/m0/s1
InChIKey 
NFARHPAOOHOWAL-AWEZNQCLSA-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)