SMTL ID : 6br3.2 (2 other biounits)

Structure of RORgt in complex with a novel inverse agonist TAK-828.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 4 residues within 4Å: Chain A: E.40, Y.44, K.47, R.55 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.40, A:Y.44 Hydrogen bonds: A:E.40, A:K.47, A:R.55, A:R.55 MPD.3: 5 residues within 4Å: Chain B: E.40, G.43, Y.44, K.47, R.55 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.44 Hydrogen bonds: B:Y.44, B:K.47, B:R.55

2 x E3V: {cis-3-[(5R)-5-[(7-fluoro-1,1-dimethyl-1H-inden-5-yl)carbamoyl]-2-methoxy-7,8-dihydro-1,6-naphthyridine-6(5H)-carbonyl]cyclobutyl}acetic acid(Non-covalent)

E3V.2: 17 residues within 4Å: Chain A: Q.22, L.23, C.56, H.59, L.60, V.97, R.100, M.101, A.104, V.112, F.113, F.114, E.115, G.116, F.124, I.136, F.137 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.23, A:A.104, A:V.112, A:F.113, A:F.114, A:F.124, A:F.124, A:F.124, A:I.136, A:F.137 Hydrogen bonds: A:F.113, A:E.115 E3V.4: 16 residues within 4Å: Chain B: Q.22, L.23, C.56, H.59, L.60, V.97, R.100, M.101, A.104, V.112, F.113, F.114, E.115, G.116, F.124, F.137 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.23, B:A.104, B:V.112, B:F.113, B:F.114, B:F.124, B:F.124, B:F.124, B:F.137 Hydrogen bonds: B:F.113, B:E.115 Halogen bonds: B:C.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kono, M. et al., Discovery of [ cis-3-({(5 R)-5-[(7-Fluoro-1,1-dimethyl-2,3-dihydro-1 H-inden-5-yl)carbamoyl]-2-methoxy-7,8-dihydro-1,6-naphthyridin-6(5 H)-yl}carbonyl)cyclobutyl]acetic Acid (TAK-828F) as a Potent, Selective, and Orally Available Novel Retinoic Acid Receptor-Related Orphan Receptor gamma t Inverse Agonist. J. Med. Chem. (2018)

Release Date

2018-03-21

Peptides

Nuclear receptor ROR-gamma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nuclear receptor ROR-gamma

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