SMTL ID : 5tbh.1

Crystal structure of mouse CARM1 in complex with inhibitor LH1236

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-tetramer

Ligands

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

M2M.1: 12 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, G.135, Y.136, N.140, E.141, H.289, W.290, K.345 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.141

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

EDO.2: 6 residues within 4Å: Chain A: A.204, D.207, E.208, R.211 Chain B: L.31, H.96 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: N.159, I.271, G.272, S.273 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: D.267, W.278, S.280 Ligand excluded by PLIP EDO.6: 11 residues within 4Å: Chain A: Y.28, M.37, E.132, P.133, M.134, G.135, E.141, H.289, W.290 Ligands: M2M.1, SAO.7 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain B: S.10, E.118, E.119, V.120, S.121, K.152 Ligands: EDO.11 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain B: S.10, E.119 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain B: D.267, W.278, S.280 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: Q.125, K.152, Y.153 Ligands: EDO.8 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, N.140, E.141, K.345 Ligands: 78K.13 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: 8 residues within 4Å: Chain C: K.151, K.152, L.154, K.155, P.156, S.157, G.158, L.235 Ligand excluded by PLIP EDO.16: 12 residues within 4Å: Chain C: Y.28, M.37, R.43, E.132, P.133, M.134, G.135, E.141, M.143, H.289, W.290 Ligands: SAO.19 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, E.141, K.345 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain C: D.267, W.278, S.280 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain D: D.267, W.278, S.280, E.285 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain D: Q.23, Y.24, F.27, Y.28, E.141 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain D: F.349, R.350 Ligand excluded by PLIP

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

PG4.4: 10 residues within 4Å: Chain A: Q.48, L.52, Q.53, H.55, Q.79, A.80 Chain D: D.332, Q.333, T.334, G.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.79

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

SAO.7: 30 residues within 4Å: Chain A: F.12, R.15, Y.24, F.25, Y.28, Q.34, M.37, M.38, 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: EDO.6 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.19: 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: EDO.16 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:Y.24, 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, C:E.132 Salt bridges: C:R.43 pi-Stacking: C:F.25

2 x 78K: (2~{R})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[[4-azanyl-1-(methoxymethyl)-2-oxidanylidene-pyrimidin-5-yl]methyl]amino]-2-azanyl-butanoic acid(Non-covalent)

78K.13: 35 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, 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, E.141, M.143, S.146, H.289, W.290 Ligands: EDO.12 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Q.34, B:C.68, B:G.69, B:A.90, B:S.91, B:V.117, B:E.118, B:E.132, B:W.290 Water bridges: B:R.15, B:G.71, B:L.73, B:E.132, B:Y.136 Salt bridges: B:R.43 pi-Stacking: B:F.25 78K.23: 34 residues within 4Å: Chain D: 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, E.141, M.143, S.146, H.289, W.290 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.34, D:C.68, D:G.69, D:A.90, D:V.117, D:E.118, D:E.132, D:E.132, D:P.133, D:W.290 Water bridges: D:R.15, D:G.71, D:Y.136 Salt bridges: D:R.43, D:E.132 pi-Stacking: D:F.25, 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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