SMTL ID : 7puq.1

CARM1 in complex with EML982

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

4 x 867: methyl 6-[4-[[~{N}-[3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]propyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate(Non-covalent)

867.1: 31 residues within 4Å: Chain A: F.12, Y.24, F.25, F.27, Y.28, Q.33, Q.34, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, Y.136, E.141, M.143, S.146, H.289, W.290, K.345, P.347 Ligands: 867.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.27, A:F.27, A:Y.136 Hydrogen bonds: A:G.69, A:E.89, A:E.89, A:A.90, A:V.117, A:E.118, A:Y.136, A:Y.136, A:E.141, A:H.289, A:K.345 Water bridges: A:R.15, A:Q.34, A:Q.34 Salt bridges: A:E.132, A:E.141 pi-Stacking: A:F.25 867.5: 32 residues within 4Å: Chain B: F.12, Y.24, F.25, F.27, Y.28, Q.33, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, Y.136, N.140, E.141, M.143, S.146, H.289, W.290, K.345, N.346, P.347 Ligands: 867.1 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.27, B:F.27, B:Y.136 Hydrogen bonds: B:G.69, B:E.89, B:E.89, B:A.90, B:V.117, B:E.118, B:M.134, B:M.134, B:E.141 Water bridges: B:Q.34 Salt bridges: B:E.132, B:E.141 pi-Stacking: B:F.25 867.7: 33 residues within 4Å: Chain C: F.12, Q.23, Y.24, F.25, F.27, Y.28, Q.33, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, Y.136, N.140, E.141, M.143, S.146, H.289, W.290, K.345, N.346, P.347 Chain D: Q.23 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.27, C:Y.136 Hydrogen bonds: C:Y.28, C:G.69, C:E.89, C:A.90, C:V.117, C:E.118, C:M.134, C:Y.136, C:Y.136, C:N.140, C:K.345, D:Q.23 Water bridges: C:R.15, C:Y.28, C:E.89 Salt bridges: C:E.132, C:E.141, C:K.345 pi-Stacking: C:F.25 867.9: 32 residues within 4Å: Chain D: F.12, Y.24, F.25, F.27, Y.28, Q.33, Q.34, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, Y.136, N.140, E.141, M.143, S.146, H.289, W.290, K.345, N.346, P.347 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.27, D:F.27, D:Y.136 Hydrogen bonds: D:Y.28, D:G.67, D:G.69, D:E.89, D:E.89, D:A.90, D:V.117, D:E.118, D:Y.136, D:N.140 Salt bridges: D:E.132, D:E.141 pi-Stacking: D:F.25

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

EDO.2: 4 residues within 4Å: Chain A: V.328, Q.330, K.337 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.337 EDO.3: 2 residues within 4Å: Chain A: K.337 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.337 EDO.4: 3 residues within 4Å: Chain A: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain B: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain C: D.267, W.278, S.280 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.285 EDO.10: 3 residues within 4Å: Chain D: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.11: 3 residues within 4Å: Chain A: L.52 Chain D: D.332, Q.333 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
A

B
B

C
C

D
D

Histone-arginine methyltransferase CARM1