8UMG: Chromodomains of human CHD1

Chromodomains of human CHD1 complexed with UNC10142. Determined by X-ray diffraction at 3.1 Å resolution. Released 23 Oct 2024.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,635
Mol. weight: 67.67 kDa
Ligands: X31
Released: 23 Oct 2024

Explore 8UMG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UMG contains 20 α-helices and 23 β-strands across 3 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
β-strand	16-25	10	2
α-helix	32-34	3
α-helix	36-41	6
β-strand	57-64	8	2
β-strand	73-75	3	2
α-helix	77-82	6
β-strand	86	1	1
α-helix	88-103	16
α-helix	110-129	20
β-strand	133-139	7	3
β-strand	140	1	4
β-strand	150-155	6	3
α-helix	160-162	3
β-strand	164-167	4	3
α-helix	168-184	17

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	5
β-strand	17-25	9	6
α-helix	37-42	6
β-strand	59-65	7	6
α-helix	70-72	3
β-strand	74-77	4	6
α-helix	78-82	5
β-strand	87	1	5
α-helix	90-107	18
α-helix	111-130	20
β-strand	134-140	7	7
β-strand	152-156	5	7
α-helix	161-163	3
β-strand	165-167	3	7
α-helix	169-173	5
α-helix	177-184	8

Chain C: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	8
β-strand	16-24	9	9
α-helix	31-34	4
α-helix	36-39	4
β-strand	44	1	4
β-strand	58-64	7	9
α-helix	69-71	3
β-strand	73-75	3	9
α-helix	77-82	6
β-strand	86	1	8
α-helix	89-95	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromodomain-helicase-DNA-binding protein 1	A, B, C	protein	187	Homo sapiens	O14646 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8UMG_1 Chromodomain-helicase-DNA-binding protein 1 (chains A, B, C)
MKKHHHHHHEEEFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQY
LIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQ
ELTDDLHKQYQIVGRIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACID
EYFSRKK

Ligands and cofactors

ID	Name	Formula	Copies
X31	1-{4-[{2-(azonan-1-yl)-6-methoxy-7-[3-(piperidin-1-yl)propoxy]quinazolin-4-yl}(…	C33 H52 N6 O3	2

Water and common crystallization additives (CL) are not listed.

Primary citation

Discovery of CHD1 Antagonists for PTEN-Deficient Prostate Cancer. Johnson, R.L., Graboski, A.L., Li, F. et al. J Med Chem (2024) 67:20056-20075. DOI 10.1021/acs.jmedchem.4c01172 · PubMed

Other PDB entries of the same protein (UniProt O14646 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9T9F 1.35 Å, Crystal structure of human CHD1 tandem chromodomain in complex with the…
9T9H 1.45 Å, Crystal structure of human CHD1 tandem chromodomain in complex with the…
9T9I 1.55 Å, Crystal structure of human CHD1 tandem chromodomain in complex with the…
5AFW 1.6 Å, Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation
4B4C 1.62 Å, Crystal structure of the DNA-binding domain of human CHD1.
9T9E 1.7 Å, Crystal structure of human CHD1 tandem chromodomain in complex with the…
9T9G 1.7 Å, Crystal structure of human CHD1 tandem chromodomain in complex with the…
4O42 1.87 Å, Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail…
4NW2 1.9 Å, Tandem chromodomains of human CHD1 in complex with Influenza virus NS1 C-terminal tail…
2B2Y 2.35 Å, Tandem chromodomains of human CHD1
2B2W 2.4 Å, Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing…
2B2T 2.45 Å, Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing…

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