7M40: Histone-binding protein RBBP4

Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4). Determined by X-ray diffraction at 1.88 Å resolution. Released 12 May 2021.

Method: X-ray diffraction
Resolution: 1.88 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,444
Mol. weight: 100.62 kDa
Ligands: YQJ
Released: 12 May 2021

Explore 7M40 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M40 contains 11 α-helices and 63 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	9-31	23
β-strand	32-39	8	1
β-strand	48-54	7	2
β-strand	61-69	9	2
β-strand	77-87	11	2
α-helix	95-98	4
β-strand	102	1	3
β-strand	104	1	4
β-strand	106	1	4
β-strand	108	1	3
α-helix	111-114	4
β-strand	115-123	9	2
β-strand	129-133	5	5
β-strand	136-143	8	5
β-strand	149-153	5	5
α-helix	154-156	3
β-strand	171-174	4	5
β-strand	183-185	3	6
β-strand	192-196	5	6
β-strand	202-206	5	6
β-strand	215-218	4	5
β-strand	221-223	3	6
β-strand	230-235	6	7
β-strand	242-247	6	7
β-strand	251-256	6	7
β-strand	267-270	4	7
β-strand	276-281	6	8
β-strand	288-293	6	8
β-strand	297-302	6	8
β-strand	311-314	4	8
β-strand	320-325	6	9
β-strand	332-337	6	9
β-strand	342-346	5	9
α-helix	347-349	3
β-strand	366-370	5	9
β-strand	377-382	6	1
β-strand	389-394	6	1
β-strand	398-404	7	1
α-helix	406-409	4

Chain B: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	32-39	8	10
β-strand	47-49	3	11
β-strand	54	1	11
β-strand	61-69	9	11
β-strand	77-87	11	11
β-strand	115-123	9	11
β-strand	129-133	5	12
β-strand	136-143	8	12
β-strand	149-153	5	12
α-helix	154-156	3
α-helix	161-162	2
β-strand	171-174	4	12
β-strand	183-185	3	13
β-strand	192-196	5	13
β-strand	202-206	5	13
β-strand	216-218	3	12
β-strand	221-223	3	13
β-strand	230-235	6	14
β-strand	242-247	6	14
β-strand	251-256	6	14
β-strand	267-270	4	14
β-strand	276-281	6	15
β-strand	288-293	6	15
β-strand	297-302	6	15
β-strand	311-314	4	15
β-strand	320-325	6	16
β-strand	332-337	6	16
β-strand	342-346	5	16
α-helix	347-349	3
β-strand	366-370	5	16
β-strand	377-382	6	10
β-strand	389-394	6	10
β-strand	398-404	7	10
α-helix	406-409	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A, B	protein	443	Homo sapiens	Q09028 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7M40_1 Histone-binding protein RBBP4 (chains A, B)
MHHHHHHSSGRENLYFQGMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEW
PSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEK
GEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPD
PSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTI
FTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFN
PYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRL
NVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVW
QMAENIYNDEDPEGSVDPEGQGS

Ligands and cofactors

ID	Name	Formula	Copies
YQJ	N~3~-{4-[3-(dimethylamino)pyrrolidin-1-yl]-6,7-dimethoxyquinazolin-2-yl}-N~1~,N…	C21 H34 N6 O2	2

Primary citation

Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4). Perveen, S., Zepeda-Velazquez, C., Abbey, M. et al. To be published.

Other PDB entries of the same protein (UniProt Q09028 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4R7A 1.85 Å, Crystal Structure of RBBP4 bound to PHF6 peptide
2XU7 1.9 Å, Structural basis for RbAp48 binding to FOG-1
5XXQ 1.9 Å, Crystal structure of RBBP4: ZNF827 and its function in telomere
6BW4 2.0 Å, Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide
9V5M 2.1 Å, The crystal structure of RBBP4-H3 complex
5Y1U 2.14 Å, Crystal structure of RBBP4 bound to AEBP2 RRK motif
4PBZ 2.15 Å, Structure of the human RbAp48-MTA1(670-695) complex
6BW3 2.2 Å, Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide
8TX8 2.2 Å, Crystal Structure of RBBP4 bound to ZNF512B peptide
3GFC 2.3 Å, Crystal Structure of Histone-binding protein RBBP4
5VTB 2.4 Å, Crystal structure of RBBP4 bound to BCL11a peptide
4PBY 2.5 Å, Structure of the human RbAp48-MTA1(656-686) complex

Browse structure collections

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