---
license: cc-by-4.0
pretty_name: GID4 (PDB 7SLZ) — GA-II Designed Ligand–Receptor Complexes
task_categories:
- tabular-regression
- graph-ml
- other
size_categories:
- 1K<n<10K
configs:
- config_name: default
  data_files:
  - split: train
    path: data/gid4_7slz.parquet
language:
- en
tags:
- chemistry
- drug-discovery
- generative-ai
- molecular-docking
- protein-ligand-complex
- targeted-protein-degradation
- GID4
- SMILES
- cheminformatics
- biology
- de-novo-design
- generative-design
- structure-based-drug-design
- synthetic
- synthetic-data
- ai-generated
- computational-chemistry
- virtual-screening
- E3-ligase
- N-degron
- 7SLZ
- CTLH-complex
- GID-complex
- E3-ubiquitin-ligase
- N-degron-pathway
- substrate-receptor
- ligase-handle
- TPD
- degrader
- small-molecule
- SDF
- genetic-algorithm
- GA-II
- autodock-vina
- TC-43
- technetium
---

# 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](https://www.rcsb.org/structure/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:

```python
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)

```python
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.