SMTL ID : 5lv2.2 (1 other biounit)

Crystal structure of mouse CARM1 in complex with inhibitor LH1246

Coordinates

PDB Format Compare

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: 28 residues within 4Å: Chain A: 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 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.34, A:G.67, A:E.89, A:A.90, A:S.91, A:V.117, A:E.118 Water bridges: A:R.15, A:G.71 Salt bridges: A:R.43 pi-Stacking: A:F.25 SAO.11: 28 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 16 PLIP interactions: 16 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:Q.34, C:G.71, C:G.71, C:E.132 Salt bridges: C:R.43 pi-Stacking: C:F.25

8 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 Hydrogen bonds: A:D.267 EDO.3: 3 residues within 4Å: Chain A: L.52 Chain D: D.332, G.335 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.332 EDO.6: 3 residues within 4Å: Chain B: K.152, Y.153 Ligands: PG4.9 No protein-ligand interaction detected (PLIP) EDO.8: 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 EDO.12: 3 residues within 4Å: Chain C: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.13: 7 residues within 4Å: Chain B: D.332, Q.333, T.334, G.335 Chain C: Q.48, L.52, Q.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.332 EDO.14: 5 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, E.141 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.141 Water bridges: C:Q.23 EDO.16: 4 residues within 4Å: Chain D: D.267, W.278, S.280, E.285 No protein-ligand interaction detected (PLIP)

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

M2M.4: 8 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, Y.136, N.140, E.141, K.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.136

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.5: 30 residues within 4Å: Chain B: 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, E.141, M.143, S.146, H.289, W.290 Ligands: PG4.7 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.43, B:R.43, B:G.67, B:E.89, B:A.90, B:V.117, B:E.118, B:E.132, B:W.290 Water bridges: B:R.15, B:Q.33, B:Q.34, B:Y.136 pi-Stacking: B:F.25, B:F.25 LHB.15: 28 residues within 4Å: Chain D: 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 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.34, D:R.43, D:R.43, D:G.69, D:A.90, D:S.91, D:V.117, D:E.118, D:E.132, D:E.132, D:W.290 Water bridges: D:R.15, D:Y.136 pi-Stacking: D:F.25

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

PG4.7: 13 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, Q.33, Y.136, N.140, E.141, K.345, N.346, F.349, Y.351 Ligands: LHB.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.136 Water bridges: B:N.36, B:Y.136, B:N.140, B:N.140 PG4.9: 10 residues within 4Å: Chain B: R.9, S.10, V.11, E.118, E.119, V.120, S.121, K.152, Y.153 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.120

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

NA.10: 8 residues within 4Å: Chain B: S.280, T.281, A.282, E.285, P.286, L.287, T.288, Q.292 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.286, B:T.288, B:Q.292

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
E

B
F

C
G

D
H

Histone-arginine methyltransferase CARM1

Related Entries With Identical Sequence