6yij

Crystal structure of the CREBBP bromodomain in complex with a benzo-diazepine ligand

Method: X-RAY DIFFRACTION

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

CREBBP

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	(4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	(4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	(4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	(4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	(4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CBP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–119； UniProt 1081–1197 Author chain B； PDBConstruct 3–119； UniProt 1081–1197 Author chain C； PDBConstruct 3–119； UniProt 1081–1197 Author chain D； PDBConstruct 3–119； UniProt 1081–1197 Author chain E； PDBConstruct 3–119； UniProt 1081–1197 Author chain F； PDBConstruct 3–119； UniProt 1081–1197 Author chain G； PDBConstruct 3–119； UniProt 1081–1197

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	6yij
Deposition date deposition_date	2020-04-01
Structure title title	Crystal structure of the CREBBP bromodomain in complex with a benzo-diazepine ligand
Keywords keywords	Bromodomain, CREBBP, small molecule, benzo-diazepine, SGC, Structural Genomics Consortium, 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.

6yij__assembly_1__model_1

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

Download this curve (.dat)

6yij__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6yij__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.55 Å
Rg (electron density)	15.43 Å
Total Rg	16.75 Å
Atom count	1021
Residues	119
Excluded volume	18448 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6yij__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6yij__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6yij__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6yij__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6yij__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6yij__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`6yij__assembly_7__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 (3)

Entity 1 Entity 1 polymer

Description description	CREBBP
Molecular weight formula_weight	14223.3 kDa
EC 编号 ec_number	2.3.1.48,2.3.1.-
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	7177

SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG

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(DE3)

Entity 2 Entity 2 non-polymer

Description description	(4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one
Molecular weight formula_weight	405.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d6yija1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.1 — Bromodomain

Domain ID domain_id	d6yija2
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	d6yijb1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.1 — Bromodomain

Domain ID domain_id	d6yijb2
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	d6yijc1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.1 — Bromodomain

Domain ID domain_id	d6yijc2
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	d6yijd_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.1 — Bromodomain

Domain ID domain_id	d6yije_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.1 — Bromodomain

Domain ID domain_id	d6yijf1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.1 — Bromodomain

Domain ID domain_id	d6yijf2
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	d6yijg_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.1 — Bromodomain

CATH v4.4 (7 domains)

Domain ID domain_id	6yijA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	6yijB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	6yijC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	6yijD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	6yijE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	6yijF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	6yijG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

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Unit-cell length a length_a	96.694 Å
Unit-cell length b length_b	96.694 Å
Unit-cell length c length_c	251.713 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	56

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	47.500 Å
R factor r_factor	0.2044
R_work r_work	0.2022
R_free r_free	0.2693

Crystal structure of the CREBBP bromodomain in complex with a benzo-diazepine ligand

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

CREBBP

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

6yij__assembly_1__model_1

6yij__assembly_1__model_1 | I(q)

6yij__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (11 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Crystal structure of the CREBBP bromodomain in complex with a benzo-diazepine ligand

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

CREBBP

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

6yij__assembly_1__model_1

6yij__assembly_1__model_1 | I(q)

6yij__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (11 domains)

CATH v4.4 (7 domains)

7. Citations (1)