SMTL ID : 5isa.1

Crystal structure of mouse CARM1 in complex with inhibitor SA0401

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x 6D5: (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azidopropyl)amino]-2-azanyl-butanoic acid(Non-covalent)

6D5.1: 32 residues within 4Å: Chain A: F.12, R.15, 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, H.289, W.290 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.34, A:Q.34, A:G.67, A:G.69, A:E.89, A:E.89, A:A.90, A:S.91, A:V.117, A:E.118 Water bridges: A:R.15 Salt bridges: A:R.43, A:E.132 pi-Stacking: A:F.25 6D5.6: 33 residues within 4Å: Chain B: F.12, R.15, Y.24, F.25, 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 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:Q.34, B:R.43, B:G.67, B:C.68, B:G.69, B:S.70, B:G.71, B:E.89, B:E.89, B:A.90, B:S.91, B:V.117, B:E.118, B:E.132, B:W.290 Water bridges: B:R.15, B:L.73, B:L.73 Salt bridges: B:R.43, B:E.132 pi-Stacking: B:F.25 6D5.9: 33 residues within 4Å: Chain C: F.12, 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, G.135, E.141, M.143, S.146, H.289, W.290 Ligands: DXE.12 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: 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.141, C:W.290 Water bridges: C:R.15, C:G.71 Salt bridges: C:R.43, C:E.132 pi-Stacking: C:F.25 6D5.15: 32 residues within 4Å: Chain D: F.12, R.15, Y.24, F.25, 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, E.141, M.143, S.146, H.289, W.290 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.34, D:G.69, D:S.70, D:G.71, D:E.89, D:E.89, D:A.90, D:V.117, D:E.118, D:E.132, D:E.132, D:E.141, D:W.290 Water bridges: D:R.15, D:L.73, D:E.132 Salt bridges: D:R.43, D:E.132 pi-Stacking: D: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 No protein-ligand interaction detected (PLIP) EDO.3: 6 residues within 4Å: Chain A: K.151, L.154, K.155, P.156, G.158, L.235 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, E.141, K.345 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.23 EDO.8: 3 residues within 4Å: Chain B: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain C: K.151, L.154, K.155, P.156, L.235 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.151, C:L.235 EDO.11: 5 residues within 4Å: Chain C: D.40, L.287, T.288, H.289, Y.291 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.291, C:Y.291 Water bridges: C:D.40, C:L.287 EDO.16: 3 residues within 4Å: Chain D: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.17: 5 residues within 4Å: Chain D: K.151, L.154, K.155, P.156, L.235 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.154, D:L.235

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

DXE.4: 7 residues within 4Å: Chain A: Y.178, F.182, V.206, D.207, F.210, Q.298, S.299 No protein-ligand interaction detected (PLIP) DXE.5: 6 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, N.140, E.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.28 Water bridges: A:Y.24 DXE.12: 8 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, Y.136, E.141, K.345 Ligands: 6D5.9 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.140, C:K.345

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

PEG.13: 4 residues within 4Å: Chain C: D.267, W.278, S.280, E.285 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.278 Water bridges: C:S.280

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

M2M.14: 7 residues within 4Å: Chain C: S.157, G.158, N.159, L.235, I.271, G.272, S.273 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.159, C:N.159

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

PG4.18: 5 residues within 4Å: Chain D: S.10, E.118, E.119, V.120, S.121 No protein-ligand interaction detected (PLIP)

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

NA.19: 5 residues within 4Å: Chain D: I.164, D.166, K.229, T.231, W.278 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cura, V. et al., Crystal structure of mouse CARM1 in complex with inhibitor SA0401. To Be Published

Release Date

2017-03-15

Peptides

Histone-arginine methyltransferase CARM1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

Histone-arginine methyltransferase CARM1