SMTL ID : 6e3g.2 (1 other biounit)

Structure of RORgt in complex with a novel agonist.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x LYS- ILE- LEU- HIS- ARG- LEU- LEU- GLN: co-activator peptide(Non-covalent)

LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN.1: 10 residues within 4Å: Chain A: K.74, F.79, M.80, Q.84, Q.87, I.88, L.91, P.238, L.239, E.242 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.74, A:F.79, A:Q.87, A:I.88, A:I.88, A:L.91, A:P.238, A:L.239 Hydrogen bonds: A:K.74, A:Q.84, A:E.242, A:E.242 Water bridges: A:E.242, A:E.242

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

EDO.2: 8 residues within 4Å: Chain A: M.51, W.55, L.129, G.130, C.131, R.220, I.223, F.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.220, A:R.220

1 x HOJ: (5R)-6-acetyl-2-methoxy-N-{4-[(2-methoxyphenyl)methoxy]phenyl}-5,6,7,8-tetrahydro-1,6-naphthyridine-5-carboxamide(Non-covalent)

HOJ.3: 20 residues within 4Å: Chain A: Q.24, L.25, W.55, C.58, H.61, L.62, M.96, V.99, R.102, M.103, A.106, V.114, F.115, F.116, E.117, F.126, L.129, I.135, I.138, H.217 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.62, A:A.106, A:V.114, A:F.126, A:I.138 Hydrogen bonds: A:F.115, A:E.117 Water bridges: A:Q.24, A:R.105, A:A.106 pi-Stacking: A:F.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yukawa, T. et al., Design, Synthesis, and Biological Evaluation of Retinoic Acid-Related Orphan Receptor gamma t (ROR gamma t) Agonist Structure-Based Functionality Switching Approach from In House ROR gamma t Inverse Agonist to ROR gamma t Agonist. J.Med.Chem. (2019)

Release Date

2019-06-12

Peptides

Nuclear receptor ROR-gamma: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Nuclear receptor ROR-gamma

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