Binder profile

09C

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

Bound to: PA1498 — pyruvate kinase

Via homolog PDB 3t07 UniProt Q6GG09 C20H16Br2N4O
Mol. weight 488.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
09C
PDB
3t07
UniProt (similar protein)
Q6GG09
Target protein
PA1498

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 488.18 Da
LogP (Crippen) 4.68
H-bond donors 4
H-bond acceptors 2
TPSA 72.71 Ų
Rotatable bonds 2
Aromatic rings 4 / 5
Heavy atoms 27
Fraction sp³ C 0.15
Formula C20H16Br2N4O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 Pass 0 violations
  • MW ≤ 500 Da 488.2
  • LogP ≤ 5 4.68
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 72.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(cc1Br)[nH]cc2[C@H]3C(=O)NCC(N3)c4c[nH]c5c4ccc(c5)Br
InChI 
InChI=1S/C20H16Br2N4O/c21-10-1-3-12-14(7-23-16(12)5-10)18-9-25-20(27)19(26-18)15-8-24-17-6-11(22)2-4-13(15)17/h1-8,18-19,23-24,26H,9H2,(H,25,27)/t18?,19-/m0/s1
InChIKey 
OXVVLWOQGFZGEO-GGYWPGCISA-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
PF02887

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA1498.

PDB 9

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

Ligand PDB entry

ChEMBL 69

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)