SMTL ID : 7jtw.1

Crystal structure of RORgt with compound (4R)-6-[(2,5-dichloro-3-{[(2R,4R)-1-(cyclopentanecarbonyl)-2-methylpiperidin-4-yl]oxy}phenyl)amino]-6-oxo-4-phenylhexanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x VK4: (4R)-6-[(2,5-dichloro-3-{[(2R,4R)-1-(cyclopentanecarbonyl)-2-methylpiperidin-4-yl]oxy}phenyl)amino]-6-oxo-4-phenylhexanoic acid(Non-covalent)

VK4.1: 20 residues within 4Å: Chain A: Q.32, W.63, C.66, H.69, L.70, A.73, M.111, A.114, V.122, F.123, F.124, E.125, F.134, L.137, L.142, I.143, F.147, S.150, H.225 Ligands: GOL.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.63, A:W.63, A:H.69, A:A.73, A:A.114, A:F.134, A:L.137, A:L.142, A:I.143 Hydrogen bonds: A:F.123, A:E.125 Water bridges: A:H.69 Salt bridges: A:H.69 pi-Cation interactions: A:H.69 Halogen bonds: A:S.150

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: C.31, Q.32, R.110, M.111, R.113 Ligands: VK4.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.113 Water bridges: A:C.31, A:Q.32, A:R.110, A:R.113 GOL.3: 8 residues within 4Å: Chain A: L.35, C.112, R.113, L.153, S.154, H.157, F.158, I.163 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.153, A:H.157, A:F.158 Water bridges: A:C.112, A:E.160 GOL.4: 4 residues within 4Å: Chain A: S.58, M.59, W.60, H.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.59, A:W.60, A:H.236

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

SO4.5: 6 residues within 4Å: Chain A: R.42, Y.115, N.116, A.117, D.118, S.154 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.116, A:A.117, A:D.118, A:S.154 Salt bridges: A:R.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakajima, R. et al., Discovery of 6-Oxo-4-phenyl-hexanoic acid derivatives as ROR gamma t inverse agonists showing favorable ADME profile. Bioorg.Med.Chem.Lett. (2021)

Release Date

2021-02-03

Peptides

RAR-related orphan receptor C isoform a variant: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RAR-related orphan receptor C isoform a variant

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