Binder profile

PCY

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

Bound to: PA4267 — 30S ribosomal protein S7

Via homolog PDB 4khp UniProt P17291 C28H38N4O8
Mol. weight 558.63 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PCY
PDB
4khp
UniProt (similar protein)
P17291
Target protein
PA4267

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 558.63 Da
LogP (Crippen) 0.75
H-bond donors 7
H-bond acceptors 10
TPSA 194.68 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 40
Fraction sp³ C 0.46
Formula C28H38N4O8

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.

Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 558.6
  • LogP ≤ 5 0.75
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 194.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cccc(c1C(=O)OC[C@]2([C@H]([C@@H]([C@]([C@@]2(C)O)([C@H](C)O)NC(=O)N(C)C)N)Nc3cccc(c3)C(=O)C)O)O
InChI 
InChI=1S/C28H38N4O8/c1-15-9-7-12-20(35)21(15)24(36)40-14-27(39)23(30-19-11-8-10-18(13-19)16(2)33)22(29)28(17(3)34,26(27,4)38)31-25(37)32(5)6/h7-13,17,22-23,30,34-35,38-39H,14,29H2,1-6H3,(H,31,37)/t17-,22-,23-,26-,27+,28-/m0/s1
InChIKey 
WVIUOSJLUCTGFK-JUJPXXQGSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00177

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA4267.

PDB 3

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

Ligand PDB entry

ChEMBL 3

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)