SMTL ID : 8g2i.1

Crystal Structure of PRMT4 with Compound YD1290

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

2 x I0B: 5'-([2-(benzylcarbamamido)ethyl]{3-[N'-(3-bromophenyl)carbamimidamido]propyl}amino)-5'-deoxyadenosine(Non-covalent)

I0B.1: 26 residues within 4Å: Chain A: Y.32, Q.38, D.44, R.47, T.48, Y.51, G.71, C.72, G.73, I.76, L.77, E.93, A.94, S.95, G.119, K.120, V.121, E.122, E.136, P.137, M.138, E.145, M.147, S.150, H.293, W.294 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:R.47, A:I.76, A:L.77, A:L.77, A:E.136, A:W.294 Hydrogen bonds: A:Y.32, A:Q.38, A:R.47, A:G.71, A:G.71, A:G.73, A:A.94, A:S.95, A:V.121, A:E.122, A:E.136, A:S.150 Water bridges: A:D.69, A:L.77 Salt bridges: A:E.136, A:E.145 pi-Stacking: A:Y.51, A:W.294 pi-Cation interactions: A:R.47 I0B.4: 26 residues within 4Å: Chain B: Y.32, Q.38, D.44, R.47, T.48, Y.51, G.71, C.72, G.73, I.76, L.77, E.93, A.94, S.95, G.119, K.120, V.121, E.122, E.136, P.137, M.138, E.145, M.147, S.150, H.293, W.294 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:R.47, B:I.76, B:L.77, B:L.77, B:E.136, B:W.294 Hydrogen bonds: B:Q.38, B:R.47, B:G.71, B:G.71, B:G.73, B:A.94, B:S.95, B:V.121, B:E.122, B:E.136, B:S.150 Water bridges: B:D.69, B:L.77 Salt bridges: B:E.136, B:E.145 pi-Stacking: B:Y.51, B:W.294 pi-Cation interactions: B:R.47

4 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 1 residues within 4Å: Chain A: H.259 No protein-ligand interaction detected (PLIP) UNX.3: 2 residues within 4Å: Chain A: D.211, Q.302 No protein-ligand interaction detected (PLIP) UNX.5: 1 residues within 4Å: Chain B: H.259 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain B: D.211, Q.302 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, Y. et al., A unique binding pocket induced by a noncanonical SAH mimic to develop potent and selective PRMT inhibitors. Acta Pharm Sin B (2023)

Release Date

2024-02-21

Peptides

Histone-arginine methyltransferase CARM1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histone-arginine methyltransferase CARM1

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