8G2H: PRMT4 with Compound YD1113

Crystal Structure of PRMT4 with Compound YD1113. Determined by X-ray diffraction at 1.49 Å resolution. Released 13 Dec 2023.

Method: X-ray diffraction
Resolution: 1.49 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,029
Mol. weight: 41.61 kDa
Ligands: YVU
Released: 13 Dec 2023

Explore 8G2H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G2H contains 16 α-helices and 21 β-strands across 1 chain. 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: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	145-153	9
α-helix	156-163	8
α-helix	166-177	12
α-helix	180-182	3
β-strand	187-191	5	1
α-helix	197-204	8
β-strand	209-214	6	1
α-helix	218-228	11
β-strand	235-239	5	1
β-strand	251-256	6	1
β-strand	260	1	2
β-strand	263	1	2
α-helix	268-274	7
α-helix	275-278	4
β-strand	279-286	8	1
β-strand	289-297	9	3
α-helix	300-308	9
α-helix	311-314	4
β-strand	318	1	4
β-strand	321	1	4
α-helix	324-326	3
α-helix	327-335	9
α-helix	338	1
β-strand	339-341	3	3
α-helix	345-347	3
β-strand	348	1	3
α-helix	351-352	2
β-strand	353-358	6	3
α-helix	364-368	5
β-strand	369-377	9	5
β-strand	382-396	15	3
β-strand	401-405	5	3
β-strand	417-428	12	3
β-strand	433-442	10	5
β-strand	448-456	9	5
β-strand	462-468	7	5
β-strand	473-474	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-arginine methyltransferase CARM1	A	protein	359	Homo sapiens	Q86X55 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8G2H_1 Histone-arginine methyltransferase CARM1 (chains A)
MHHHHHHSSGRENLYFQGRTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHT
DFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGK
VEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQ
LYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLE
AKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCL
FQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTT

Ligands and cofactors

ID	Name	Formula	Copies
YVU	5'-S-[2-(benzylcarbamamido)ethyl]-5'-thioadenosine	C20 H25 N7 O4 S	1

Water and common crystallization additives (UNX, NA, GOL) are not listed.

Primary citation

A unique binding pocket induced by a noncanonical SAH mimic to develop potent and selective PRMT inhibitors. Deng, Y., Song, X., Iyamu, I.D. et al. Acta Pharm Sin B (2023) 13:4893-4905. DOI 10.1016/j.apsb.2023.07.022 · PubMed

Other PDB entries of the same protein (UniProt Q86X55 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DVR 1.54 Å, Crystal structure of human CARM1 with (R)-SKI-72
8SIG 1.78 Å, Crystal Structure of PRMT4 with Compound YD1-288
6S7A 1.86 Å, Crystal structure of CARM1 in complex with inhibitor AA175
8UQH 1.87 Å, X-ray crystal structure of PRMT4 bound to compound YD-1130
5U4X 1.88 Å, Coactivator-associated arginine methyltransferase 1 with TP-064
6ARJ 1.92 Å, Crystal structure of CARM1 with EPZ022302 and SAH
5DX1 1.93 Å, Crystal structure of CARM1, sinefungin, and PABP1 peptide (R455)
5DX8 1.94 Å, Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R455)
5DXJ 1.95 Å, Crystal structure of CARM1 and sinefungin
9O6H 1.97 Å, The Structure of PRMT4 in complex with SGC8172
4IKP 2.0 Å, Crystal structure of coactivator-associated arginine methyltransferase 1 with…
6ARV 2.0 Å, Crystal structure of CARM1 with Compound 2 and SAH

Browse structure collections

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