SMTL ID : 8uqh.1

X-ray crystal structure of PRMT4 bound to compound YD-1130

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-octamer

Ligands

8 x X9L: 5'-S-(2-{[(3-bromophenyl)methyl]amino}ethyl)-5'-thioadenosine

X9L.1: 20 residues within 4Å: Chain A: Y.11, F.12, Y.15, M.24, R.30, G.54, E.76, A.77, S.78, G.102, K.103, V.104, E.105, E.119, M.121, E.128, M.130, S.133, H.276, W.277 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.276, A:W.277 Hydrogen bonds: A:A.77, A:V.104, A:E.105, A:E.119, A:S.133 Water bridges: A:Q.21, A:S.78 pi-Stacking: A:F.12, A:W.277 X9L.2: 21 residues within 4Å: Chain B: Y.11, F.12, Y.15, M.24, D.27, R.30, G.54, E.76, A.77, S.78, G.102, K.103, V.104, E.105, E.119, M.121, E.128, M.130, S.133, H.276, W.277 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:H.276, B:W.277 Hydrogen bonds: B:A.77, B:S.78, B:V.104, B:E.105, B:E.119, B:S.133 Water bridges: B:Q.21, B:S.78 pi-Stacking: B:F.12, B:W.277 Halogen bonds: B:D.27 X9L.3: 20 residues within 4Å: Chain C: Y.11, F.12, Y.15, G.54, G.56, E.76, A.77, S.78, G.102, K.103, V.104, E.105, E.119, M.121, Y.123, E.128, M.130, S.133, H.276, W.277 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Y.123, C:H.276, C:W.277 Hydrogen bonds: C:G.56, C:A.77, C:V.104, C:E.105, C:E.119, C:S.133 Water bridges: C:Q.21, C:G.54, C:S.78, C:Q.308 pi-Stacking: C:F.12, C:W.277 X9L.4: 19 residues within 4Å: Chain D: Y.11, F.12, Y.15, D.27, G.54, E.76, A.77, S.78, G.102, K.103, V.104, E.105, E.119, M.121, E.128, M.130, S.133, H.276, W.277 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:H.276, D:W.277 Hydrogen bonds: D:A.77, D:V.104, D:E.105, D:E.119, D:S.133 Water bridges: D:Q.21, D:Q.21, D:S.78 pi-Stacking: D:F.12, D:W.277 Halogen bonds: D:D.27 X9L.5: 20 residues within 4Å: Chain E: Y.11, F.12, Y.15, M.24, R.30, G.54, E.76, A.77, S.78, G.102, K.103, V.104, E.105, E.119, M.121, E.128, M.130, S.133, H.276, W.277 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:H.276, E:W.277 Hydrogen bonds: E:A.77, E:V.104, E:E.105, E:E.119, E:S.133 Water bridges: E:Q.21, E:S.78 pi-Stacking: E:F.12, E:W.277 X9L.6: 21 residues within 4Å: Chain F: Y.11, F.12, Y.15, M.24, D.27, R.30, G.54, E.76, A.77, S.78, G.102, K.103, V.104, E.105, E.119, M.121, E.128, M.130, S.133, H.276, W.277 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:H.276, F:W.277 Hydrogen bonds: F:A.77, F:S.78, F:V.104, F:E.105, F:E.119, F:S.133 Water bridges: F:Q.21, F:S.78 pi-Stacking: F:F.12, F:W.277 Halogen bonds: F:D.27 X9L.7: 20 residues within 4Å: Chain G: Y.11, F.12, Y.15, G.54, G.56, E.76, A.77, S.78, G.102, K.103, V.104, E.105, E.119, M.121, Y.123, E.128, M.130, S.133, H.276, W.277 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:Y.123, G:H.276, G:W.277 Hydrogen bonds: G:G.56, G:A.77, G:V.104, G:E.105, G:E.119, G:S.133 Water bridges: G:Q.21, G:G.54, G:S.78, G:Q.308 pi-Stacking: G:F.12, G:W.277 X9L.8: 19 residues within 4Å: Chain H: Y.11, F.12, Y.15, D.27, G.54, E.76, A.77, S.78, G.102, K.103, V.104, E.105, E.119, M.121, E.128, M.130, S.133, H.276, W.277 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:H.276, H:W.277 Hydrogen bonds: H:A.77, H:V.104, H:E.105, H:E.119, H:S.133 Water bridges: H:Q.21, H:Q.21, H:S.78 pi-Stacking: H:F.12, H:W.277 Halogen bonds: H:D.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, Y. et al., An Adenosine Analogue Library Reveals Insights into Active Sites of Protein Arginine Methyltransferases and Enables the Discovery of a Selective PRMT4 Inhibitor. J.Med.Chem. (2024)

Release Date

2025-04-02

Peptides

Histone-arginine methyltransferase CARM1: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Histone-arginine methyltransferase CARM1

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