SMTL ID : 6w6d.1

Crystal Structure of Human Protein arginine N-methyltransferase 6 (PRMT6) in complex with SGC6870 inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain A: M.61, R.67, G.91, A.92, G.93, T.94, I.96, L.97, V.112, E.113, A.114, S.115, I.117, G.139, P.140, V.141, E.142, E.156, M.167, S.170 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:H.58, A:T.94, A:A.114, A:S.115, A:V.141, A:E.142, A:E.156, A:E.156, A:S.170 Water bridges: A:L.97, A:L.97, A:S.115, A:S.115 Salt bridges: A:R.67 SAH.3: 20 residues within 4Å: Chain B: M.61, R.67, G.91, A.92, G.93, T.94, I.96, L.97, V.112, E.113, A.114, S.115, I.117, G.139, P.140, V.141, E.142, E.156, M.167, S.170 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:H.58, B:T.94, B:A.114, B:S.115, B:V.141, B:E.142, B:E.156, B:E.156, B:S.170 Water bridges: B:L.97, B:L.97, B:S.115, B:S.115 Salt bridges: B:R.67

2 x T9A: (5R)-4-(5-bromothiophene-2-carbonyl)-5-(3,5-dimethylphenyl)-7-methyl-1,3,4,5-tetrahydro-2H-1,4-benzodiazepin-2-one(Non-covalent)

T9A.2: 17 residues within 4Å: Chain A: W.157, M.158, G.159, Y.160, G.161, H.164, E.165, L.168, L.192, L.257, I.291, F.293, L.344, L.345, P.346, L.354, M.374 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.157, A:M.158, A:E.165, A:L.168, A:L.192, A:L.192, A:L.257, A:F.293, A:L.344 Hydrogen bonds: A:G.159, A:G.161 pi-Stacking: A:Y.160 T9A.4: 17 residues within 4Å: Chain B: W.157, M.158, G.159, Y.160, G.161, H.164, E.165, L.168, L.192, L.257, I.291, F.293, L.344, L.345, P.346, L.354, M.374 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.157, B:M.158, B:E.165, B:L.168, B:L.192, B:L.192, B:L.257, B:F.293, B:L.344 Hydrogen bonds: B:G.159, B:G.161 pi-Stacking: B:Y.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, Y. et al., A First-in-Class, Highly Selective and Cell-Active Allosteric Inhibitor of Protein Arginine Methyltransferase 6. J.Med.Chem. (2021)

Release Date

2020-04-29

Peptides

Protein arginine N-methyltransferase 6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein arginine N-methyltransferase 6

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