SMTL ID : 5k8x.1

Crystal structure of mouse CARM1 in complex with inhibitor U3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

4 x 6ZH: [[[(~{E})-3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]prop-2-enyl]amino]-azanyl-methylidene]azanium(Non-covalent)

6ZH.1: 27 residues within 4Å: Chain A: F.12, R.15, Y.24, F.25, Y.28, 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, E.141, M.143, S.146, H.289, W.290 Ligands: PG4.8 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.28, A:G.67, A:G.69, A:E.89, A:A.90, A:S.91, A:V.117, A:E.118, A:E.132, A:H.289 Water bridges: A:R.15, A:Q.34 Salt bridges: A:E.132, A:E.141 pi-Stacking: A:F.25 6ZH.10: 25 residues within 4Å: Chain B: F.12, R.15, Y.24, F.25, Y.28, 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, E.141, M.143, S.146, H.289, W.290 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Y.28, B:Y.28, B:G.69, B:E.89, B:E.89, B:A.90, B:S.91, B:V.117, B:E.118, B:E.132 Water bridges: B:H.289 Salt bridges: B:E.132, B:E.141 pi-Stacking: B:F.25 6ZH.16: 26 residues within 4Å: Chain C: F.12, R.15, Y.24, F.25, Y.28, 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, E.141, M.143, S.146, H.289, W.290 Ligands: M2M.25 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:Y.28, C:Y.28, C:G.69, C:E.89, C:E.89, C:A.90, C:S.91, C:S.91, C:V.117, C:E.118, C:E.132 Water bridges: C:R.15, C:Q.34 Salt bridges: C:E.132, C:E.141 pi-Stacking: C:F.25 6ZH.26: 25 residues within 4Å: Chain D: F.12, R.15, Y.24, F.25, Y.28, 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, E.141, M.143, S.146, H.289, W.290 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.28, D:Y.28, D:G.69, D:E.89, D:E.89, D:A.90, D:V.117, D:E.118, D:E.132 Water bridges: D:R.15 Salt bridges: D:E.132, D:E.141 pi-Stacking: D:F.25

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

EDO.2: 2 residues within 4Å: Chain A: D.267, W.278 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.267, A:S.280 EDO.3: 6 residues within 4Å: Chain A: D.40, L.287, T.288, H.289, Y.291, Y.351 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.351, A:Y.351 EDO.4: 4 residues within 4Å: Chain A: F.27, Y.30, S.32, Q.33 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: F.12, E.18, A.21, V.22, F.25, K.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.116 Water bridges: A:E.18 EDO.11: 6 residues within 4Å: Chain B: F.12, E.18, A.21, V.22, F.25, K.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.116 EDO.12: 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) EDO.13: 6 residues within 4Å: Chain B: N.36, D.40, L.287, T.288, H.289, Y.291 No protein-ligand interaction detected (PLIP) EDO.17: 4 residues within 4Å: Chain C: P.283, T.284, E.285, P.286 No protein-ligand interaction detected (PLIP) EDO.18: 3 residues within 4Å: Chain C: T.217, F.218, D.219 2 PLIP interactions: 2 interactions with chain C Water bridges: C:F.218, C:D.219 EDO.27: 3 residues within 4Å: Chain D: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.28: 6 residues within 4Å: Chain B: L.258, P.300 Chain C: Q.39 Chain D: T.183, F.187 Ligands: DXE.23 No protein-ligand interaction detected (PLIP) EDO.29: 5 residues within 4Å: Chain D: E.118, E.119, V.120, S.121, K.152 No protein-ligand interaction detected (PLIP) EDO.30: 4 residues within 4Å: Chain D: P.283, T.284, E.285, P.286 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.284 EDO.31: 5 residues within 4Å: Chain D: Y.24, F.27, Y.28, E.141, K.345 3 PLIP interactions: 3 interactions with chain D Water bridges: D:N.140, D:N.140, D:K.345

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

PEG.6: 7 residues within 4Å: Chain A: S.157, G.158, N.159, L.235, I.271, G.272, S.273 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.159, A:N.159 PEG.7: 8 residues within 4Å: Chain A: K.151, K.152, L.154, K.155, P.156, S.157, G.158, L.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.158 PEG.19: 7 residues within 4Å: Chain C: D.57, S.157, G.158, N.159, I.271, G.272, S.273 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.157, C:G.272 PEG.20: 6 residues within 4Å: Chain C: F.182, V.206, D.207, F.210, Q.298, S.299 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.298 PEG.21: 4 residues within 4Å: Chain C: D.267, W.278, S.280, E.285 2 PLIP interactions: 2 interactions with chain C Water bridges: C:W.278, C:W.278

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

PG4.8: 13 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, Q.33, G.135, Y.136, N.140, E.141, H.289, W.290, K.345 Ligands: 6ZH.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.141

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

PE8.9: 4 residues within 4Å: Chain A: V.328, Q.330, K.337, S.339 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.337

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

DXE.14: 4 residues within 4Å: Chain B: D.267, W.278, S.280, E.285 No protein-ligand interaction detected (PLIP) DXE.15: 8 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, Y.136, N.140, E.141, K.345 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.140 DXE.22: 7 residues within 4Å: Chain C: K.151, L.154, K.155, P.156, G.158, L.235, E.236 No protein-ligand interaction detected (PLIP) DXE.23: 9 residues within 4Å: Chain B: L.258, F.302 Chain C: M.38, Q.39, Y.41 Chain D: F.187, Q.190, F.193 Ligands: EDO.28 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Water bridges: B:F.302 Hydrogen bonds: D:Q.190 DXE.24: 6 residues within 4Å: Chain C: F.27, Y.30, S.32, Q.33, N.36 Chain D: N.346 No protein-ligand interaction detected (PLIP) DXE.32: 7 residues within 4Å: Chain D: N.36, M.37, D.40, L.287, T.288, H.289, Y.291 No protein-ligand interaction detected (PLIP)

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

M2M.25: 12 residues within 4Å: Chain C: Y.24, F.27, Y.28, Q.33, G.135, Y.136, N.140, E.141, H.289, W.290, K.345 Ligands: 6ZH.16 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.28 Water bridges: C:Y.136, C:N.140

Links

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Citation

Cura, V. et al., Crystal structure of mouse CARM1 in complex with inhibitor U3. To Be Published

Release Date

2017-06-21

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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