SMTL ID : 6d2l.1

Crystal structure of human CARM1 with (S)-SKI-72

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x FTG: (2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-[(benzylamino)methyl]-N-[2-(4-hydroxyphenyl)ethyl]hexanamide(Non-covalent)

FTG.1: 25 residues within 4Å: Chain A: F.5, F.7, Y.8, Q.14, M.18, R.23, G.47, G.49, I.52, E.69, A.70, S.71, G.95, K.96, V.97, E.98, E.112, P.113, M.114, Y.116, E.121, M.123, S.126, H.269, W.270 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.7, A:Y.8, A:I.52, A:Y.116, A:E.121 Hydrogen bonds: A:G.47, A:A.70, A:S.71, A:S.71, A:S.71, A:V.97, A:E.98, A:E.112, A:E.121, A:E.121, A:S.126 Water bridges: A:R.23 pi-Stacking: A:F.5 FTG.6: 26 residues within 4Å: Chain B: F.5, Y.8, Q.14, M.18, R.23, G.47, C.48, I.52, V.68, E.69, A.70, S.71, G.95, K.96, V.97, E.98, E.112, P.113, M.114, Y.116, N.120, E.121, M.123, S.126, H.269, W.270 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.8, B:I.52, B:Y.116, B:E.121 Hydrogen bonds: B:G.47, B:A.70, B:S.71, B:S.71, B:S.71, B:V.97, B:E.98, B:E.112, B:N.120, B:E.121, B:E.121, B:S.126 pi-Stacking: B:F.5 FTG.7: 23 residues within 4Å: Chain C: F.5, Y.8, M.18, R.23, G.47, C.48, I.52, V.68, E.69, A.70, S.71, G.95, K.96, V.97, E.98, E.112, P.113, M.114, E.121, M.123, S.126, H.269, W.270 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.8, C:I.52 Hydrogen bonds: C:G.47, C:A.70, C:S.71, C:S.71, C:S.71, C:V.97, C:E.98, C:E.112, C:E.121, C:E.121, C:S.126 pi-Stacking: C:F.5 FTG.8: 25 residues within 4Å: Chain D: F.5, F.7, Y.8, Q.14, M.18, R.23, G.47, C.48, V.68, E.69, A.70, S.71, G.95, K.96, V.97, E.98, E.112, P.113, M.114, Y.116, E.121, M.123, S.126, H.269, W.270 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.7, D:Y.8, D:Y.116, D:E.121 Hydrogen bonds: D:G.47, D:A.70, D:S.71, D:S.71, D:S.71, D:V.97, D:E.98, D:E.112, D:E.121, D:E.121, D:S.126 pi-Stacking: D:F.5 FTG.11: 27 residues within 4Å: Chain E: Y.4, F.5, Y.8, Q.14, M.17, M.18, R.23, G.47, C.48, G.49, I.52, V.68, E.69, A.70, S.71, G.95, K.96, V.97, E.98, E.112, P.113, M.114, E.121, M.123, S.126, H.269, W.270 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:Y.8, E:I.52 Hydrogen bonds: E:G.47, E:A.70, E:S.71, E:V.97, E:E.98, E:E.121, E:E.121, E:S.126 Water bridges: E:Q.14, E:S.71, E:E.112 pi-Stacking: E:F.5, E:F.5 FTG.14: 26 residues within 4Å: Chain F: F.5, Y.8, Q.14, M.18, R.23, G.47, C.48, G.49, I.52, V.68, E.69, A.70, S.71, G.95, K.96, V.97, E.98, E.112, P.113, M.114, Y.116, E.121, M.123, S.126, H.269, W.270 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:Y.8, F:I.52, F:Y.116, F:E.121 Hydrogen bonds: F:G.47, F:A.70, F:S.71, F:S.71, F:S.71, F:V.97, F:E.98, F:N.120, F:E.121, F:E.121, F:S.126 Water bridges: F:N.120, F:E.121 pi-Stacking: F:F.5

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: K.206, S.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.148, A:S.207 SO4.9: 2 residues within 4Å: Chain D: K.206, S.207 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.207, D:S.207 SO4.12: 3 residues within 4Å: Chain E: K.206, S.207, W.245 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.207, E:S.207 Water bridges: E:H.148

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: D.247, W.258, S.260 No protein-ligand interaction detected (PLIP) GOL.4: 2 residues within 4Å: Chain A: I.251, T.256 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.256, A:T.256

3 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.10: 2 residues within 4Å: Chain D: H.235, S.236 No protein-ligand interaction detected (PLIP) UNX.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cai, X.C. et al., A chemical probe of CARM1 alters epigenetic plasticity against breast cancer cell invasion. Elife (2019)

Release Date

2018-05-23

Peptides

Histone-arginine methyltransferase CARM1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

E
C

F
D

Histone-arginine methyltransferase CARM1

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