SMTL ID : 5is9.1

Crystal structure of mouse CARM1 in complex with inhibitor SA0375

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x 6D3: (2S)-2-amino-4-[(3-{4-[(2S)-2-amino-2-carboxyethyl]-1H-1,2,3-triazol-1-yl}propyl){[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}amino]butanoic acid (non-preferred name)(Non-covalent)

6D3.1: 33 residues within 4Å: Chain A: F.12, Y.24, F.25, Y.28, Q.34, M.37, R.43, D.65, G.67, C.68, G.69, S.70, I.72, L.73, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, M.134, G.135, Y.136, N.140, E.141, M.143, S.146, H.289, W.290 Ligands: EDO.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.28 Hydrogen bonds: A:Q.34, A:G.67, A:E.89, A:E.89, A:A.90, A:V.117, A:E.118, A:E.132, A:Y.136, A:N.140, A:E.141, A:W.290 Water bridges: A:R.15, A:G.71, A:E.132 Salt bridges: A:R.43, A:E.132 pi-Stacking: A:F.25, A:W.290 6D3.12: 36 residues within 4Å: Chain B: F.12, R.15, Y.24, F.25, F.27, Y.28, Q.34, M.37, R.43, G.67, C.68, G.69, S.70, I.72, L.73, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, S.131, E.132, P.133, M.134, G.135, Y.136, N.140, E.141, M.143, S.146, H.289, W.290 Ligands: EDO.13 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:Y.28, B:Y.136 Hydrogen bonds: B:Y.28, B:Q.34, B:C.68, B:S.70, B:E.89, B:E.89, B:A.90, B:S.91, B:V.117, B:E.118, B:E.132, B:Y.136, B:N.140, B:E.141, B:E.141, B:W.290 Water bridges: B:R.15, B:L.73, B:E.132 Salt bridges: B:R.43, B:E.132 pi-Stacking: B:F.25 6D3.18: 36 residues within 4Å: Chain C: F.12, R.15, Y.24, F.25, F.27, Y.28, Q.34, M.37, R.43, G.67, C.68, G.69, S.70, G.71, I.72, L.73, 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 Ligands: EDO.19 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:Y.28 Hydrogen bonds: C:Q.34, C:G.67, C:E.89, C:E.89, C:A.90, C:S.91, C:V.117, C:E.118, C:Y.136, C:Y.136, C:N.140, C:W.290 Water bridges: C:R.15, C:Q.34, C:G.71, C:E.141 Salt bridges: C:R.43, C:E.132 pi-Stacking: C:F.25 6D3.24: 36 residues within 4Å: Chain D: F.12, Y.24, F.25, F.27, Y.28, Q.34, M.37, R.43, D.65, G.67, C.68, G.69, S.70, I.72, L.73, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, S.131, E.132, P.133, M.134, G.135, Y.136, N.140, E.141, M.143, S.146, H.289, W.290 Ligands: EDO.27 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:Y.136 Hydrogen bonds: D:Y.28, D:Q.34, D:G.67, D:S.70, D:E.89, D:E.89, D:A.90, D:S.91, D:V.117, D:E.118, D:Y.136, D:N.140, D:E.141 Water bridges: D:R.15, D:L.73, D:E.132 Salt bridges: D:R.43, D:E.132 pi-Stacking: D:F.25

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

EDO.2: 6 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, E.141 Ligands: 6D3.1 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: D.267, W.278, S.280 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: D.40, L.287, T.288, H.289, Y.291, Y.351 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: A.21, V.22, F.25, K.116 Ligand excluded by PLIP EDO.6: 1 residues within 4Å: Chain A: R.202 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, E.141, K.345 Ligands: 6D3.12 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: L.287, T.288, H.289, Y.291, Y.351 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: K.151, L.154, K.155, P.156 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, E.141, K.345 Ligands: 6D3.18 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain C: D.267, W.278, S.280 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: D.332, Q.333, T.334, G.335 Chain C: Q.48, L.52, Q.79 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain C: I.271, G.272, S.273 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain C: D.40, L.287, T.288, H.289, Y.291 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain D: D.267, W.278, S.280, E.285 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain D: D.207, Q.298, N.340, L.341 Ligands: PEG.28 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain D: Q.23, Y.24, F.27, K.345 Ligands: 6D3.24 Ligand excluded by PLIP

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 7 residues within 4Å: Chain A: Q.48, L.52, Q.79 Chain D: D.332, Q.333, T.334, G.335 No protein-ligand interaction detected (PLIP) PEG.8: 7 residues within 4Å: Chain A: Y.178, F.182, V.206, D.207, F.210, Q.298, S.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.207, A:D.207, A:S.299 PEG.16: 3 residues within 4Å: Chain B: D.267, W.278, S.280 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.280, B:E.285 PEG.28: 8 residues within 4Å: Chain B: P.191 Chain D: D.207, Q.298, S.299, S.338, S.339, N.340 Ligands: EDO.26 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.298, D:S.339 Water bridges: D:Q.298

2 x DXE: 1,2-DIMETHOXYETHANE(Non-covalent)(Non-functional Binders)

DXE.9: 6 residues within 4Å: Chain A: G.158, N.159, L.235, I.271, G.272, S.273 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.159 DXE.10: 2 residues within 4Å: Chain A: S.339 Ligands: PG4.11 No protein-ligand interaction detected (PLIP)

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

PG4.11: 5 residues within 4Å: Chain A: V.328, Q.330, K.337, S.339 Ligands: DXE.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.337

1 x M2M: 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE(Non-covalent)

M2M.17: 9 residues within 4Å: Chain B: D.207, R.211, Q.298, S.326, I.327, V.328, S.339, N.340, L.341 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cura, V. et al., Crystal structure of mouse CARM1 in complex with inhibitor SA0375. To Be Published

Release Date

2017-03-15

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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