4e47

SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine

Method: X-RAY DIFFRACTION

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

Histone-lysine N-methyltransferase SETD7

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	S-ADENOSYLMETHIONINE × 1 (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 BETA-MERCAPTOETHANOL × 1 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	S-ADENOSYLMETHIONINE × 1 (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	S-ADENOSYLMETHIONINE × 1 (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	S-ADENOSYLMETHIONINE × 1 (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SETD7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 109–366 Author chain B； PDBConstruct 1–258； UniProt 109–366 Author chain C； PDBConstruct 1–258； UniProt 109–366 Author chain D； PDBConstruct 1–258； UniProt 109–366

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	4e47
Deposition date deposition_date	2012-03-12
Structure title title	SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine
Keywords keywords	;ternary complex, SET domain, methyltransferase, inhibitor, S-adenosylmethionine, chromatin regulator, chromosomal protein, nucleus, transcription, transcription regulation, transferase, Structural Genomics Consortium, SGC, TRANSFERASE-TRANSFERASE INHIBITOR complex ;; TRANSFERASE/TRANSFERASE INHIBITOR
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.

4e47__assembly_1__model_1

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

Download this curve (.dat)

4e47__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4e47__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.65 Å
Rg (electron density)	19.66 Å
Total Rg	20.54 Å
Atom count	1982
Residues	246
Excluded volume	34759 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4e47__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4e47__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4e47__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4e47__assembly_4__model_1`	monomeric （1）	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)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase SETD7
Molecular weight formula_weight	29684.0 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8934

QYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKSGPEAPEWYQVELKAFQATQQKHHHHHH

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

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	(R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide
Molecular weight formula_weight	438.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	857

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4e47a1
Class class	b — All beta proteins
Fold Fold fold	b.76 — open-sided beta-meander
Superfamily Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	d4e47a2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.1 — Histone lysine methyltransferases

Domain ID domain_id	d4e47a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4e47b1
Class class	b — All beta proteins
Fold Fold fold	b.76 — open-sided beta-meander
Superfamily Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	d4e47b2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.1 — Histone lysine methyltransferases

Domain ID domain_id	d4e47b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4e47c1
Class class	b — All beta proteins
Fold Fold fold	b.76 — open-sided beta-meander
Superfamily Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	d4e47c2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.1 — Histone lysine methyltransferases

Domain ID domain_id	d4e47c3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4e47d1
Class class	b — All beta proteins
Fold Fold fold	b.76 — open-sided beta-meander
Superfamily Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	d4e47d2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.1 — Histone lysine methyltransferases

Domain ID domain_id	d4e47d3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	4e47A01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	4e47A02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	4e47B01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	4e47B02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	4e47C01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	4e47C02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	4e47D01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	4e47D02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

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Unit-cell length a length_a	117.343 Å
Unit-cell length b length_b	133.799 Å
Unit-cell length c length_c	136.865 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	39.880 Å
R factor r_factor	0.1616
R_work r_work	0.1595
R_free r_free	0.2007

SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine

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

Histone-lysine N-methyltransferase SETD7

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4e47__assembly_1__model_1

4e47__assembly_1__model_1 | I(q)

4e47__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)

SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine

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

Histone-lysine N-methyltransferase SETD7

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

4e47__assembly_1__model_1

4e47__assembly_1__model_1 | I(q)

4e47__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)