SMTL ID : 7ppq.1

CARM1 in complex with EML736

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

LSK.1: 37 residues within 4Å: Chain A: F.12, R.15, Y.24, F.25, F.27, Y.28, Q.33, Q.34, M.37, R.43, 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, F.349 Chain B: Q.23 Ligands: EDO.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.27, A:Y.136, A:F.349, A:F.349 Hydrogen bonds: A:Y.24, A:Y.28, A:E.89, A:A.90, A:V.117, A:E.118, A:M.134, A:N.140, A:E.141 Water bridges: A:R.15, A:Q.33, A:Q.34, A:Q.34, A:S.131, A:E.132, A:E.132, A:Y.136 Salt bridges: A:E.141 pi-Stacking: A:F.25 LSK.4: 34 residues within 4Å: Chain B: 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, L.344, K.345, N.346, P.347, F.349 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:F.27, B:P.347, B:F.349, B:F.349 Hydrogen bonds: B:Y.24, B:Y.28, B:Q.33, B:G.67, B:G.67, B:G.69, B:E.89, B:A.90, B:V.117, B:E.118, B:E.132, B:N.140, B:E.141 Water bridges: B:R.15, B:Q.34, B:Q.34 Salt bridges: B:E.132, B:E.141 pi-Stacking: B:F.25 LSK.7: 34 residues within 4Å: Chain C: F.12, Q.23, 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, F.349 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:F.27, C:F.349 Hydrogen bonds: C:Y.24, C:Y.24, C:Y.28, C:Y.28, C:Q.33, C:E.89, C:E.89, C:A.90, C:V.117, C:E.118, C:E.132, C:N.140 Water bridges: C:R.15, C:Q.34, C:Q.34, C:Y.136 Salt bridges: C:E.132, C:E.141 pi-Stacking: C:F.25 LSK.10: 33 residues within 4Å: Chain D: 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, L.344, K.345, N.346, P.347, F.349 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:F.27, D:Y.136, D:P.347, D:F.349 Hydrogen bonds: D:Y.28, D:G.69, D:E.89, D:E.89, D:A.90, D:S.91, D:V.117, D:E.118, D:M.134, D:N.140, D:E.141 Water bridges: D:Y.28, D:Y.28, D:S.131 Salt bridges: D:E.132, D:E.141 pi-Stacking: D:F.25, D:F.349

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

EDO.2: 3 residues within 4Å: Chain A: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.3: 6 residues within 4Å: Chain A: Y.24, F.27, Y.28, E.141, K.345 Ligands: LSK.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.141 EDO.5: 3 residues within 4Å: Chain B: D.267, W.278, S.280 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.267, B:S.280, B:E.285 EDO.6: 6 residues within 4Å: Chain A: Q.39 Chain B: F.187, Q.190, F.193 Chain D: L.258, F.302 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.39, B:Q.190, B:Q.190 EDO.8: 6 residues within 4Å: Chain C: K.151, L.154, K.155, P.156, S.157, L.235 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.154 EDO.9: 3 residues within 4Å: Chain C: D.267, W.278, S.280 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.267 Water bridges: C:S.280 EDO.11: 3 residues within 4Å: Chain D: D.267, W.278, S.280 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

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