SMTL ID : 7pu8.1

CARM1 in complex with EML980

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-tetramer

Ligands

4 x 4R7: methyl 6-[4-[[N-[2-[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate(Non-covalent)

4R7.1: 37 residues within 4Å: Chain A: 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 Chain B: Q.23 Ligands: EDO.2, EDO.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.27, A:F.27, A:Y.136, A:F.349 Hydrogen bonds: A:Y.28, A:E.89, A:A.90, A:V.117, A:E.118, A:M.134, A:Y.136, A:E.141 Water bridges: A:R.15, A:Q.34 Salt bridges: A:E.132, A:E.141 pi-Stacking: A:F.25, A:F.349 4R7.4: 34 residues within 4Å: Chain B: F.12, 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 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.27, B:Y.28, B:Y.136, B:P.347 Hydrogen bonds: B:G.67, B:E.89, B:A.90, B:V.117, B:E.118, B:Y.136, B:N.140 Water bridges: B:R.15, B:Q.33, B:Q.33, B:Q.33, B:Q.33 Salt bridges: B:E.132, B:E.141 pi-Stacking: B:F.25, B:F.349, B:F.349 4R7.5: 36 residues within 4Å: Chain C: F.12, Q.23, 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 Ligands: EDO.6 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:F.27, C:F.27, C:Y.28, C:Y.136 Hydrogen bonds: C:Y.28, C:G.67, C:G.69, C:A.90, C:V.117, C:E.118, C:M.134, C:Y.136, C:N.140 Water bridges: C:Y.28, C:Q.34 Salt bridges: C:E.132, C:E.141 pi-Stacking: C:F.25, C:F.349, C:F.349 4R7.7: 35 residues within 4Å: Chain D: F.12, 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 Ligands: EDO.8 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:F.27, D:Y.28, D:Y.136, D:P.347 Hydrogen bonds: D:Y.28, D:G.67, D:G.69, D:A.90, D:S.91, D:S.91, 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, D:F.349, D:F.349

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

EDO.2: 6 residues within 4Å: Chain A: Y.136, V.215, Y.291, F.349, Y.351 Ligands: 4R7.1 No protein-ligand interaction detected (PLIP) EDO.3: 6 residues within 4Å: Chain A: Q.23, Y.24, F.27, E.141, K.345 Ligands: 4R7.1 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, K.345 Ligands: 4R7.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.23 EDO.8: 4 residues within 4Å: Chain D: Q.23, Y.24, F.27 Ligands: 4R7.7 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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