SMTL ID : 5tbj.1

Crystal structure of mouse CARM1 in complex with inhibitor LH1452

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-tetramer

Ligands

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

LHD.1: 30 residues within 4Å: Chain A: 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, E.141, M.143, S.146, H.289, W.290 Ligands: EDO.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.28, A:Q.33, A:Q.34, A:A.90, A:V.117, A:E.118, A:E.132 Water bridges: A:R.15, A:Y.28, A:Y.136 pi-Stacking: A:F.25, A:Y.28 LHD.6: 30 residues within 4Å: Chain B: 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, W.290 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.28, B:Q.33, B:A.90, B:S.91, B:V.117, B:E.118, B:E.132 Water bridges: B:R.15, B:Q.34, B:Q.34, B:R.43 pi-Stacking: B:F.25 LHD.13: 31 residues within 4Å: Chain C: 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, E.141, M.143, S.146, H.289, W.290 Ligands: EDO.16 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Y.28, C:Q.33, C:G.69, C:A.90, C:S.91, C:V.117, C:E.118, C:E.132 Water bridges: C:R.15, C:Y.24, C:E.132, C:Y.136 pi-Stacking: C:F.25, C:Y.28 LHD.18: 31 residues within 4Å: Chain D: 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, E.141, M.143, S.146, H.289, W.290 Ligands: EDO.19 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Y.28, D:Q.33, D:E.89, D:A.90, D:S.91, D:V.117, D:E.118, D:E.132 Water bridges: D:R.15, D:Y.24, D:Q.34, D:R.43, D:E.132, D:Y.136 pi-Stacking: D:F.25, D:Y.28

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

PEG.2: 8 residues within 4Å: Chain A: Q.39, D.40, Y.41, L.287, T.288, H.289, Y.291, Y.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.39, A:Y.351, A:Y.351 PEG.11: 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 C Hydrogen bonds: C:Q.79 PEG.14: 7 residues within 4Å: Chain C: Q.39, D.40, L.287, T.288, H.289, Y.291, Y.351 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.291 PEG.15: 4 residues within 4Å: Chain C: N.159, I.271, G.272, S.273 No protein-ligand interaction detected (PLIP)

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

EDO.3: 4 residues within 4Å: Chain A: L.52 Chain D: D.332, T.334, G.335 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.52 EDO.4: 7 residues within 4Å: Chain A: Y.24, F.27, Y.28, Y.136, N.140, E.141 Ligands: LHD.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.141 EDO.7: 1 residues within 4Å: Chain B: R.49 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, K.345 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.23 Water bridges: B:Q.23 EDO.9: 2 residues within 4Å: Chain B: N.233, E.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.233 EDO.12: 3 residues within 4Å: Chain B: D.267, W.278, S.280 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.267, B:S.280 EDO.16: 7 residues within 4Å: Chain C: Y.24, F.27, Y.28, Y.136, E.141, F.349 Ligands: LHD.13 No protein-ligand interaction detected (PLIP) EDO.17: 3 residues within 4Å: Chain C: D.267, W.278, S.280 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.285 EDO.19: 7 residues within 4Å: Chain D: Y.24, F.27, Y.28, Y.136, N.140, E.141 Ligands: LHD.18 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.140, D:E.141 EDO.20: 2 residues within 4Å: Chain D: Y.136, F.349 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.136 EDO.21: 3 residues within 4Å: Chain D: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP)

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

DXE.5: 4 residues within 4Å: Chain A: D.267, W.278, S.280, E.285 No protein-ligand interaction detected (PLIP)

1 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.10: 8 residues within 4Å: Chain B: R.9, S.10, E.118, E.119, V.120, S.121, K.152, Y.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.153

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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