Tc-43/GID4_7SLZ_20260620

GID4 (PDB 7SLZ) — GA-II Designed Ligand–Receptor Complexes

Why this target matters. GID4 is one of the very few usable E3 handles beyond cereblon and VHL, and the degrader field's reliance on just two ligases is currently its central bottleneck.

1,567 de novo, generative-AI–designed small-molecule ligands docked into the substrate-binding pocket of human GID4 (Glucose-Induced Degradation protein 4), each provided as a protein–ligand complex in PDB format.

GID4 is the substrate-recognition subunit of the human CTLH E3 ubiquitin-ligase complex and an emerging handle for targeted protein degradation / molecular glues. Receptor coordinates are based on PDB 7SLZ (crystal structure of GID4, Structural Genomics Consortium).

Dataset summary

Complex files	1,567 (*_complex.pdb)
Unique ligand SMILES	1,497
Receptor	GID4 substrate-binding β-barrel (chain A, ≈ residues 125–289)
Generator	Technetium GA-II pocket-conditioned generative platform
Generation date	2026-06-20

Each file is self-contained — receptor structure, the ligand's 3D docked pose, and a 2D↔3D atom map all travel inside the single PDB.

Property profile

The library was generated within a drug-like envelope and every pose clears a docking-energy bar. Physicochemical ranges below are computed over the 1,497 unique structures; docking energy is from the generation/docking pipeline.

Property	Range	Median
Docking energy	≤ −8.0 kcal/mol (down to ≈ −13.5)	—
Molecular weight	323 – 499 Da	420
cLogP	0.0 – 5.0	2.4
TPSA	34 – 130 Ų	86
Fsp3 (fraction sp³ C)	0.15 – 0.81	0.36
H-bond donors	1 – 6	2
H-bond acceptors	1 – 11	4
Rotatable bonds	2 – 10	5

The set sits in Lipinski/Veber-friendly space (MW ≤ 500, cLogP ≤ 5, rotatable bonds ≤ 10) with notable three-dimensional character (median Fsp3 0.36) — appropriate for GID4's shallow, partly peptidic substrate pocket.

File format

Filenames follow <MW>_7SLZ_II<id>_complex.pdb (<MW> = rounded molecular weight; <id> = compound id).

Record	Content
REMARK SMILES <smiles>	the bound ligand (2D structure)
REMARK SMILES IDX <pos> <serial> …	map of each SMILES heavy-atom position ↔ its HETATM serial (the 2D↔3D key)
HETATM (resname LIG)	ligand 3D pose
ATOM	GID4 receptor heavy atoms

Quick start (tabular index)

A browsable, machine-readable table (data/gid4_7slz.parquet) ships every ligand with its canonical SMILES, source complex filename, and RDKit physicochemical descriptors (mol_weight, clogp, tpsa, fsp3, h_bond_donors, h_bond_acceptors, rotatable_bonds, ring_count, num_heavy_atoms). It powers the Dataset Viewer above and loads in one line:

from datasets import load_dataset

ds = load_dataset("Tc-43/GID4_7SLZ_20260620", split="train")
print(ds[0])          # compound_id, smiles, complex_file, descriptors ...
df = ds.to_pandas()

The full 3D docked poses live in GID4_7SLZ_20260620.zip (one *_complex.pdb per row, joinable on complex_file / compound_id).

Usage (3D poses)

import glob

def read_complex(path):
    smiles, idx = None, {}
    with open(path) as fh:
        for line in fh:
            if line.startswith("REMARK SMILES IDX"):
                toks = line.split()[3:]            # flat list of (smiles_pos, hetatm_serial)
                for i in range(0, len(toks), 2):
                    idx[int(toks[i])] = int(toks[i+1])
            elif line.startswith("REMARK SMILES"):
                smiles = line.split(None, 2)[2].strip()
    return smiles, idx                              # idx[smiles_atom_position] -> HETATM serial

for f in glob.glob("GID4_7SLZ_20260620/*.pdb"):
    smi, idx = read_complex(f)
    # ... map any SMILES atom to its 3D coordinate via idx -> HETATM serial

A combined SMILES index (GID4_7SLZ_20260620.smi, SMILES<TAB>compound-id) is included for quick cheminformatics use.

Provenance & intended use

• These are computationally generated designs and docked poses — not experimentally validated binders. No claim of activity is made.
• Intended for machine-learning, cheminformatics, generative-model benchmarking, and docking-pose research on a well-defined TPD target.

Citation

Generated by Technetium Therapeutics (GA-II platform). Receptor template: RCSB PDB 7SLZ.