9dty

Crystal structure of PRT3789 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB

Method: X-RAY DIFFRACTION

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

Isoform Short of Probable global transcription activator SNF2L2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 40	von Hippel-Lindau disease tumor suppressor × 10 （P40337） Elongin-C × 10 （Q15369） Elongin-B × 10 （Q15370） ;(4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 10 CITRIC ACID × 5 ACETATE ION × 1 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMCA2_HUMAN
Isoform	P51531-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–120； UniProt 1373–1491 Author chain E； PDBConstruct 2–120； UniProt 1373–1491 Author chain I； PDBConstruct 2–120； UniProt 1373–1491 Author chain M； PDBConstruct 2–120； UniProt 1373–1491 Author chain Q； PDBConstruct 2–120； UniProt 1373–1491 Author chain U； PDBConstruct 2–120； UniProt 1373–1491 Author chain Y； PDBConstruct 2–120； UniProt 1373–1491 Author chain c； PDBConstruct 2–120； UniProt 1373–1491 Author chain g； PDBConstruct 2–120； UniProt 1373–1491 Author chain k； PDBConstruct 2–120； UniProt 1373–1491

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 40	Isoform Short of Probable global transcription activator SNF2L2 × 10 （P51531） Elongin-C × 10 （Q15369） Elongin-B × 10 （Q15370） ;(4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 10 CITRIC ACID × 5 ACETATE ION × 1 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VHL_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–161； UniProt 54–213 Author chain F； PDBConstruct 2–161； UniProt 54–213 Author chain J； PDBConstruct 2–161； UniProt 54–213 Author chain N； PDBConstruct 2–161； UniProt 54–213 Author chain R； PDBConstruct 2–161； UniProt 54–213 Author chain V； PDBConstruct 2–161； UniProt 54–213 Author chain Z； PDBConstruct 2–161； UniProt 54–213 Author chain d； PDBConstruct 2–161； UniProt 54–213 Author chain h； PDBConstruct 2–161； UniProt 54–213 Author chain l； PDBConstruct 2–161； UniProt 54–213

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 40	Isoform Short of Probable global transcription activator SNF2L2 × 10 （P51531） von Hippel-Lindau disease tumor suppressor × 10 （P40337） Elongin-B × 10 （Q15370） ;(4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 10 CITRIC ACID × 5 ACETATE ION × 1 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOC_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–96； UniProt 17–112 Author chain G； PDBConstruct 1–96； UniProt 17–112 Author chain K； PDBConstruct 1–96； UniProt 17–112 Author chain O； PDBConstruct 1–96； UniProt 17–112 Author chain S； PDBConstruct 1–96； UniProt 17–112 Author chain W； PDBConstruct 1–96； UniProt 17–112 Author chain a； PDBConstruct 1–96； UniProt 17–112 Author chain e； PDBConstruct 1–96； UniProt 17–112 Author chain i； PDBConstruct 1–96； UniProt 17–112 Author chain m； PDBConstruct 1–96； UniProt 17–112

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 40	Isoform Short of Probable global transcription activator SNF2L2 × 10 （P51531） von Hippel-Lindau disease tumor suppressor × 10 （P40337） Elongin-C × 10 （Q15369） ;(4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 10 CITRIC ACID × 5 ACETATE ION × 1 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOB_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–104； UniProt 1–104 Author chain H； PDBConstruct 1–104； UniProt 1–104 Author chain L； PDBConstruct 1–104； UniProt 1–104 Author chain P； PDBConstruct 1–104； UniProt 1–104 Author chain T； PDBConstruct 1–104； UniProt 1–104 Author chain X； PDBConstruct 1–104； UniProt 1–104 Author chain b； PDBConstruct 1–104； UniProt 1–104 Author chain f； PDBConstruct 1–104； UniProt 1–104 Author chain j； PDBConstruct 1–104； UniProt 1–104 Author chain n； PDBConstruct 1–104； UniProt 1–104

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_id	9dty
Deposition date deposition_date	2024-10-02
Structure title title	Crystal structure of PRT3789 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB
Keywords keywords	SMARCA2, VHL, PROTAC, ternary complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-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.

9dty__assembly_1__model_1

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

Download this curve (.dat)

9dty__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9dty__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	68.68 Å
Rg (electron density)	69.21 Å
Total Rg	69.28 Å
Atom count	36861
Residues	4465
Excluded volume	656130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9dty__assembly_1__model_1`	40-meric （40）	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 (8)

Entity 1 Entity 1 polymer

Description description	Isoform Short of Probable global transcription activator SNF2L2
Molecular weight formula_weight	13991.1 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M,Q,U,Y,c,g,k
Atom count atom_count	36947

SAEKLSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQKIAKE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	von Hippel-Lindau disease tumor suppressor
Molecular weight formula_weight	18615.2 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,J,N,R,V,Z,d,h,l

GMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 polymer

Description description	Elongin-C
Molecular weight formula_weight	10843.4 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,K,O,S,W,a,e,i,m

MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 4 Entity 4 polymer

Description description	Elongin-B
Molecular weight formula_weight	11748.4 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,L,P,T,X,b,f,j,n

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 5 Entity 5 non-polymer

Description description	;(4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ;
Molecular weight formula_weight	891.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 6 Entity 6 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

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Unit-cell length a length_a	183.960 Å
Unit-cell length b length_b	203.630 Å
Unit-cell length c length_c	206.950 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	40

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.190 Å
Low-resolution limit resolution_low	49.480 Å
R factor r_factor	0.2574
R_work r_work	0.2559
R_free r_free	0.2848

Crystal structure of PRT3789 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB

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

Isoform Short of Probable global transcription activator SNF2L2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

von Hippel-Lindau disease tumor suppressor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9dty__assembly_1__model_1

9dty__assembly_1__model_1 | I(q)

9dty__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)