SMTL ID : 5tbi.1

Crystal structure of mouse CARM1 in complex with inhibitor LH1427

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: Q.48, L.52 Chain D: D.332, Q.333, T.334, G.335 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: I.271, G.272, S.273 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: D.40, L.287, T.288, H.289, Y.291 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: D.267, W.278, S.280 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, E.141, K.345 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: K.59, D.60, K.61 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, E.141, K.345 Ligands: 78V.11 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain B: D.267, W.278, S.280 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain C: Y.178, F.182, V.206, D.207, F.210, Q.298 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, E.141, K.345 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain C: D.40, L.287, T.288, H.289, Y.291 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: K.151, L.154, K.155, P.156 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: D.267, W.278, S.280 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain C: T.56, D.57, K.61, S.273 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain D: Q.23, Y.24, F.27, E.141, K.345 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain D: Q.125, K.152, Y.153 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain D: D.267, W.278, S.280 Ligand excluded by PLIP

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

SAO.7: 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 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.34, A:G.67, A:G.69, A:E.89, A:A.90, A:S.91, A:S.91, A:V.117, A:E.118 Water bridges: A:R.15, A:G.71, A:E.132 Salt bridges: A:R.43 pi-Stacking: A:F.25 SAO.18: 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 13 PLIP interactions: 13 interactions with chain C 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 Water bridges: C:R.15, C:G.71, C:E.132 Salt bridges: C:R.43 pi-Stacking: C:F.25

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.8: 12 residues within 4Å: Chain B: R.9, S.10, P.114, G.115, K.116, E.118, E.119, V.120, S.121, Q.125, K.152, Y.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.125

2 x 78V: 4-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]ethylamino]-1-(methoxymethyl)pyrimidin-2-one(Non-covalent)

78V.11: 31 residues within 4Å: Chain B: F.12, R.15, Y.24, F.25, F.27, Y.28, Q.33, Q.34, M.37, G.67, C.68, 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.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.34, B:E.89, B:E.89, B:A.90, B:V.117, B:E.118, B:E.141 Water bridges: B:R.15 pi-Stacking: B:F.25 78V.22: 29 residues within 4Å: Chain D: F.12, R.15, 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, E.141, M.143, S.146, H.289, W.290 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:Q.34, D:G.69, D:E.89, D:E.89, D:A.90, D:S.91, D:V.117, D:E.118, D:E.141 Water bridges: D:R.15 pi-Stacking: D:F.25

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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