← Back to search
8x7h

Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1).

Method: X-RAY DIFFRACTION
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucose-induced degradation protein 4 homolog

Homo sapiens

UniProt Q8IVV7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Bromodomain-containing protein 4 × 1 （O60885） ;~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide ; × 1 GLYCEROL × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Bromodomain-containing protein 4 × 1 （O60885） ;~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide ; × 1 GLYCEROL × 4 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Bromodomain-containing protein 4 × 1 （O60885） ;~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide ; × 1 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Bromodomain-containing protein 4 × 1 （O60885） ;~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide ; × 1 GLYCEROL × 3 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6ccr 7q4y 7q4y 7slz 7u3e 7u3e 7u3f 7u3g 7u3h 7u3i 7u3i 7u3j

24 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6cct 6ccu 6cd8 6cd8 6cd9 6cdc 6cdg 6wzx 6wzx 6wzz 7nsc 7q50

18 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name GID4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–167； UniProt 124–289 Author chain C； PDBConstruct 2–167； UniProt 124–289 Author chain E； PDBConstruct 2–167； UniProt 124–289 Author chain G； PDBConstruct 2–167； UniProt 124–289

Bromodomain-containing protein 4

Homo sapiens

UniProt O60885

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Glucose-induced degradation protein 4 homolog × 1 （Q8IVV7） ;~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide ; × 1 GLYCEROL × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Glucose-induced degradation protein 4 homolog × 1 （Q8IVV7） ;~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide ; × 1 GLYCEROL × 4 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Glucose-induced degradation protein 4 homolog × 1 （Q8IVV7） ;~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide ; × 1 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Glucose-induced degradation protein 4 homolog × 1 （Q8IVV7） ;~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide ; × 1 GLYCEROL × 3 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2i8n 2oss 2ouo 2yel 2yem 2yem 3mxf 3p5o 3svf 3svg 3u5j 3u5k

655 assemblies; showing the first 12

Homodimer
5khm 6djc 7dhs 7l9m 7la9 7la9 7la9 7mr5 7mr6 7mr7

10 assemblies

Homotetramer

None

Other homooligomers
8wxy 8wy3 8wy7

3 assemblies

Heteromeric or nucleic-acid complex
2lsp 2mjv 2n3k 2ncz 2nd0 2nd1 2nnu 2nnu 3uvw 3uvx 3uvy 3uw9

111 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name BRD4_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–126； UniProt 44–168 Author chain D； PDBConstruct 2–126； UniProt 44–168 Author chain F； PDBConstruct 2–126； UniProt 44–168 Author chain H； PDBConstruct 2–126； UniProt 44–168

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8x7h
Deposition date deposition_date2023-11-24
Structure title titleCrystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1).
Keywords keywordsubiquitin ligase, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8x7h__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8x7h__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

8x7h__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）25.71 Å
Rg (electron density)25.47 Å
Total Rg26.11 Å
Atom count2083
Residues267
Excluded volume36051 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8x7h__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 8x7h__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 8x7h__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 8x7h__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

▶

7. Citations (1)