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9hyb

CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Elongin-B

Homo sapiens

UniProt Q15370

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1lm8 1lqb 1lqb 1vcb 1vcb 1vcb 1vcb 2c9w 2izv 2jz3 2ma9 3dcg

479 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ELOB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–104； UniProt 1–104 Author chain D； PDBConstruct 1–104； UniProt 1–104 Author chain G； PDBConstruct 1–104； UniProt 1–104 Author chain J； PDBConstruct 1–104； UniProt 1–104

Elongin-C

Homo sapiens

UniProt Q15369

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1lm8 1lqb 1lqb 1vcb 1vcb 1vcb 1vcb 2c9w 2izv 2ma9 3dcg 3dcg

468 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ELOC_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–97； UniProt 17–112 Author chain E； PDBConstruct 2–97； UniProt 17–112 Author chain H； PDBConstruct 2–97； UniProt 17–112 Author chain K； PDBConstruct 2–97； UniProt 17–112

von Hippel-Lindau disease tumor suppressor

Homo sapiens

UniProt P40337

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） Probable global transcription activator SNF2L2 × 1 （P51531） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1lm8 1lqb 1lqb 1vcb 1vcb 1vcb 1vcb 3zrc 3zrc 3zrc 3zrc 3zrf

364 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VHL_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 3–162； UniProt 54–213 Author chain F； PDBConstruct 3–162； UniProt 54–213 Author chain I； PDBConstruct 3–162； UniProt 54–213 Author chain L； PDBConstruct 3–162； UniProt 54–213

Probable global transcription activator SNF2L2

Homo sapiens

UniProt P51531

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2dat 5dkc 5dkh 5dkh 5dkh 7z78 7z78 7z78 8qjt 8qjt 8qjt 9ayq

34 assemblies; showing the first 12

Homodimer
6haz

1 assemblies

Homotetramer

None

Other homooligomers
9du0

1 assemblies

Heteromeric or nucleic-acid complex
6eg2 6eg3 6hax 6hax 6hay 6hay 7z6l 7z76 7z77 9dty 9hyb 9hyb

27 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name SMCA2_HUMAN
Isoform P51531-2
PDB entities 4
Chains and sequence ranges Author chain M； PDBConstruct 3–123； UniProt 1373–1493 Author chain N； PDBConstruct 3–123； UniProt 1373–1493 Author chain O； PDBConstruct 3–123； UniProt 1373–1493 Author chain P； PDBConstruct 3–123； UniProt 1373–1493

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id9hyb
Deposition date deposition_date2025-01-09
Last revision last_revision2025-11-12
Structure title titleCRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3
Keywords keywordsBROMODOMAIN, VCB, E3-LIGASE, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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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.

9hyb__assembly_1__model_1

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

Download this curve (.dat)

9hyb__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.

9hyb__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）31.87 Å
Rg (electron density)32.06 Å
Total Rg32.50 Å
Atom count7437
Residues448
Excluded volume66008 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9hyb__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 9hyb__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 9hyb__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 9hyb__assembly_4__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

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7. Citations (1)