SMTL ID : 5lv2.1 (1 other biounit)

Crystal structure of mouse CARM1 in complex with inhibitor LH1246

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-tetramer

Ligands

2 x SAO: 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine(Non-covalent)

SAO.1: 29 residues within 4Å: Chain A: F.12, R.15, Y.24, F.25, Y.28, Q.34, M.37, R.43, D.65, V.66, 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.143, S.146 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.34, A:G.67, A:G.67, A:G.69, A:E.89, A:E.89, A:A.90, A:S.91, A:V.117, A:E.118 Water bridges: A:Q.34, A:G.71 Salt bridges: A:R.43 pi-Stacking: A:F.25 SAO.6: 29 residues within 4Å: Chain C: F.12, R.15, Y.24, F.25, Y.28, Q.34, M.37, R.43, D.65, 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.143, S.146 Ligands: DXE.10 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Q.34, C:G.67, C:G.69, C:E.89, C:E.89, C:A.90, C:S.91, C:V.117, C:E.118 Water bridges: C:R.15, C:G.71 Salt bridges: C:R.43 pi-Stacking: C:F.25

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

EDO.2: 3 residues within 4Å: Chain A: D.267, W.278, S.280 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.280 EDO.4: 6 residues within 4Å: Chain B: Y.24, F.27, Y.28, Y.136, E.141, K.345 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.345 Water bridges: B:S.20, B:Q.321 EDO.5: 3 residues within 4Å: Chain B: D.267, W.278, S.280 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.285 EDO.8: 3 residues within 4Å: Chain C: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.13: 3 residues within 4Å: Chain D: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP)

2 x LHB: 5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]methyl]-4-azanyl-1-(methoxymethyl)pyrimidin-2-one(Non-covalent)

LHB.3: 28 residues within 4Å: Chain B: F.12, R.15, Y.24, F.25, Y.28, 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, E.141, M.143, S.146, H.289, W.290 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.24, B:Q.34, B:G.67, B:A.90, B:S.91, B:S.91, B:V.117, B:E.118, B:E.132, B:H.289 Water bridges: B:R.15, B:Y.136 pi-Stacking: B:F.25 LHB.11: 30 residues within 4Å: Chain D: F.12, R.15, Y.24, F.25, 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, W.290 Ligands: PEG.14 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:R.43, D:R.43, D:A.90, D:V.117, D:E.118, D:E.132, D:E.132, D:W.290 Water bridges: D:R.15, D:Q.34, D:S.91, D:Y.136 pi-Stacking: D:F.25

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

PG4.7: 10 residues within 4Å: Chain B: D.332, Q.333, T.334, G.335 Chain C: Q.48, L.52, H.55, Q.79, A.80 Chain D: G.195 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.79 Water bridges: C:Q.79 PG4.12: 6 residues within 4Å: Chain D: S.10, E.118, E.119, V.120, S.121, K.152 No protein-ligand interaction detected (PLIP)

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

M2M.9: 9 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, Y.136, N.140, E.141, K.345 Ligands: DXE.10 No protein-ligand interaction detected (PLIP)

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

DXE.10: 12 residues within 4Å: Chain C: Y.28, M.37, E.132, P.133, M.134, G.135, Y.136, E.141, H.289, W.290 Ligands: SAO.6, M2M.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.290 Water bridges: C:Y.136

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

PEG.14: 10 residues within 4Å: Chain D: Q.23, Y.24, F.27, Y.28, Y.136, N.140, E.141, K.345, F.349 Ligands: LHB.11 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.23, D:Y.28 Water bridges: D:Y.136, D:Y.136, D:K.345

1 x NA: SODIUM ION(Non-functional Binders)

NA.15: 8 residues within 4Å: Chain D: S.280, T.281, A.282, E.285, P.286, L.287, T.288, Q.292 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.281, D:Q.292 Water bridges: D:T.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halby, L. et al., Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors. Philos.Trans.R.Soc.Lond.B Biol.Sci. (2018)

Release Date

2017-09-20

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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