SMTL ID : 7pv6.2 (1 other biounit)

CARM1 in complex with EML734

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x LRZ: methyl 6-[3-[[~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]carbamimidoyl]amino]propylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate(Non-covalent)

LRZ.1: 35 residues within 4Å: Chain A: F.9, Y.21, F.22, F.24, Y.25, Q.30, Q.31, M.34, R.40, G.64, G.66, V.85, E.86, A.87, S.88, G.112, K.113, V.114, E.115, E.129, P.130, M.131, G.132, Y.133, N.137, E.138, M.140, S.143, H.286, W.287, K.342, N.343, P.344, F.346 Ligands: EDO.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.24, A:P.344 Hydrogen bonds: A:Y.25, A:Y.25, A:Q.31, A:G.64, A:E.86, A:A.87, A:S.88, A:V.114, A:E.115, A:E.129, A:N.137 Salt bridges: A:E.129 pi-Stacking: A:F.22, A:Y.133 LRZ.6: 34 residues within 4Å: Chain B: F.9, Y.21, F.22, F.24, Y.25, Q.30, Q.31, M.34, R.40, G.64, G.66, V.85, E.86, A.87, S.88, G.112, K.113, V.114, E.115, E.129, P.130, M.131, G.132, Y.133, N.137, E.138, M.140, S.143, H.286, W.287, K.342, N.343, P.344, F.346 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.24, B:Y.133, B:P.344 Hydrogen bonds: B:Y.21, B:Q.31, B:G.64, B:G.66, B:E.86, B:E.86, B:A.87, B:S.88, B:V.114, B:E.115, B:E.129, B:N.137, B:E.138, B:E.138 Water bridges: B:R.12 Salt bridges: B:E.129 pi-Stacking: B:F.22, B:F.346 LRZ.7: 35 residues within 4Å: Chain C: F.9, Y.21, F.22, F.24, Y.25, Q.30, Q.31, M.34, R.40, G.64, G.66, V.85, E.86, A.87, S.88, G.112, K.113, V.114, E.115, E.129, P.130, M.131, G.132, Y.133, N.137, E.138, M.140, S.143, H.286, W.287, K.342, N.343, P.344, F.346 Ligands: EDO.9 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.24, C:P.344 Hydrogen bonds: C:Y.25, C:Y.25, C:Q.31, C:G.64, C:E.86, C:A.87, C:S.88, C:V.114, C:E.115, C:E.129, C:N.137 Salt bridges: C:E.129 pi-Stacking: C:F.22, C:Y.133 LRZ.12: 34 residues within 4Å: Chain D: F.9, Y.21, F.22, F.24, Y.25, Q.30, Q.31, M.34, R.40, G.64, G.66, V.85, E.86, A.87, S.88, G.112, K.113, V.114, E.115, E.129, P.130, M.131, G.132, Y.133, N.137, E.138, M.140, S.143, H.286, W.287, K.342, N.343, P.344, F.346 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:F.24, D:Y.133, D:P.344 Hydrogen bonds: D:Y.21, D:Q.31, D:G.64, D:G.66, D:E.86, D:E.86, D:A.87, D:S.88, D:V.114, D:E.115, D:E.129, D:N.137, D:E.138, D:E.138 Water bridges: D:R.12 Salt bridges: D:E.129 pi-Stacking: D:F.22, D:F.346

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: D.264, W.275 No protein-ligand interaction detected (PLIP) EDO.3: 3 residues within 4Å: Chain A: Q.20, F.24 Ligands: LRZ.1 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: Y.38, V.39, P.283 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain C: D.264, W.275 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain C: Q.20, F.24 Ligands: LRZ.7 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain C: Y.38, V.39, P.283 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 6 residues within 4Å: Chain A: Q.45, L.49, Q.50, H.52, Q.76, A.77 No protein-ligand interaction detected (PLIP) PG4.11: 6 residues within 4Å: Chain C: Q.45, L.49, Q.50, H.52, Q.76, A.77 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iannelli, G. et al., Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach. J.Med.Chem. (2022)

Release Date

2022-04-06

Peptides

Histone-arginine methyltransferase CARM1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

Histone-arginine methyltransferase CARM1

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