SMTL ID : 5ntc.1

Crystal structure of mouse CARM1 in complex with inhibitor SA0678

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Y.24, F.27, Y.28, E.141 No protein-ligand interaction detected (PLIP) EDO.2: 3 residues within 4Å: Chain A: D.219, I.220, R.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.221, A:R.221 Water bridges: A:I.220 EDO.3: 1 residues within 4Å: Chain A: F.349 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, E.141 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.28, B:E.141 Water bridges: B:E.141 EDO.10: 4 residues within 4Å: Chain B: W.265, A.282, P.283, T.284 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain B: K.152, Y.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.152 EDO.12: 3 residues within 4Å: Chain B: K.238, E.239, G.240 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.240 Water bridges: B:E.239 EDO.13: 4 residues within 4Å: Chain A: S.103, N.104, N.105 Chain B: D.197 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.197, B:D.197, A:N.104 EDO.16: 6 residues within 4Å: Chain C: Q.39, D.40, L.287, T.288, H.289, Y.291 No protein-ligand interaction detected (PLIP) EDO.17: 1 residues within 4Å: Chain C: W.278 No protein-ligand interaction detected (PLIP) EDO.18: 4 residues within 4Å: Chain C: P.283, T.284, E.285, P.286 1 PLIP interactions: 1 interactions with chain C Water bridges: C:L.287 EDO.19: 6 residues within 4Å: Chain C: G.135, Y.136, E.141, H.289, W.290 Ligands: 6L7.21 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.289, C:W.290 Water bridges: C:E.141, C:E.141 EDO.22: 3 residues within 4Å: Chain D: Q.23, Y.24, F.27 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.23

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

PEG.4: 6 residues within 4Å: Chain A: P.283, T.284, E.285, P.286, L.287 Ligands: M2M.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.287 PEG.23: 7 residues within 4Å: Chain A: Q.48, L.52, Q.79 Chain D: D.332, Q.333, T.334, G.335 No protein-ligand interaction detected (PLIP)

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

DXE.5: 4 residues within 4Å: Chain A: K.229, D.267, W.278, S.280 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.166 DXE.20: 7 residues within 4Å: Chain B: D.332, Q.333, T.334, G.335 Chain C: Q.48, L.52, Q.79 No protein-ligand interaction detected (PLIP)

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

M2M.6: 9 residues within 4Å: Chain A: Q.39, D.40, Y.41, L.287, T.288, H.289, Y.291, Y.351 Ligands: PEG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.351 Water bridges: A:Y.41

3 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.7: 12 residues within 4Å: Chain A: Y.24, F.25, E.118, E.141, R.142, M.143, E.145, S.146, E.239, H.243, Q.321 Ligands: 6L7.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.146, A:E.239, A:E.239, A:E.239, A:H.243 Water bridges: A:S.146 B3P.14: 12 residues within 4Å: Chain B: A.21, Y.24, F.25, E.118, E.141, R.142, M.143, E.145, S.146, E.239, Q.321 Ligands: 6L7.15 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.141, B:R.142, B:E.145, B:S.146, B:E.239, B:E.239 Water bridges: B:E.118, B:E.118, B:S.146, B:S.146 B3P.24: 13 residues within 4Å: Chain D: A.21, Y.24, F.25, E.118, E.141, R.142, M.143, E.145, S.146, E.239, H.243, Q.321 Ligands: 6L7.25 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:E.145 Hydrogen bonds: D:Y.24, D:R.142, D:R.142, D:E.145, D:E.145, D:E.239, D:H.243 Water bridges: D:E.118, D:E.118, D:Q.321, D:Q.321

4 x 6L7: [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-azaniumylethyl)-[(3~{S})-3-azaniumyl-4-oxidanyl-4-oxidanylidene-butyl]azanium(Non-covalent)

6L7.8: 29 residues within 4Å: Chain A: Y.24, F.25, Y.28, Q.34, M.37, M.38, 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, E.141, M.143, S.146 Ligands: B3P.7 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:Y.24, A:Y.28, A:Q.34, A:Q.34, A:G.67, A:E.89, A:E.89, A:A.90, A:S.91, A:V.117, A:E.118, A:E.132 Water bridges: A:Y.28, A:W.290 Salt bridges: A:R.43, A:E.132 pi-Stacking: A:F.25, A:F.25 pi-Cation interactions: A:Y.28 6L7.15: 28 residues within 4Å: Chain B: 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, M.134, E.141, M.143, S.146 Ligands: B3P.14 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Y.28, B:Q.34, B:Q.34, B:G.67, B:E.89, B:E.89, B:A.90, B:S.91, B:V.117, B:E.118, B:E.132 Water bridges: B:Y.28 Salt bridges: B:R.43, B:E.132 pi-Stacking: B:F.25, B:F.25 pi-Cation interactions: B:Y.28 6L7.21: 30 residues within 4Å: Chain C: 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.134, E.141, M.143, S.146, W.290 Ligands: EDO.19 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:Y.28, C:Q.34, 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, C:E.132 Salt bridges: C:R.43, C:E.132 pi-Stacking: C:F.25 6L7.25: 29 residues within 4Å: Chain D: Y.24, F.25, Y.28, Q.34, M.37, M.38, 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, E.141, M.143, S.146 Ligands: B3P.24 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Y.24, D:Y.28, D:Q.34, D:G.67, D:S.70, D:E.89, D:E.89, D:A.90, D:S.91, D:V.117, D:E.118, D:E.132 Water bridges: D:Y.28, D:G.71 Salt bridges: D:R.43, D:E.132 pi-Stacking: D:F.25, D:F.25 pi-Cation interactions: D:Y.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cura, V. et al., Crystal structure of mouse CARM1 in complex with inhibitor SA0678. To Be Published

Release Date

2018-05-30

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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