SMTL ID : 6o3z.1

Crystal structure of RORgt with 3-cyano-N-(3-{[(3S)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl]methyl}-5-fluoro-2-methylphenyl)benzamide (compound 1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x LKY: 3-cyano-N-(3-{[(3S)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl]methyl}-5-fluoro-2-methylphenyl)benzamide(Non-covalent)

LKY.1: 20 residues within 4Å: Chain A: Q.32, L.33, L.38, W.63, C.66, H.69, L.70, M.111, R.113, A.114, V.122, F.123, F.124, F.134, L.142, I.143, I.146, F.147, S.150, H.225 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.33, A:W.63, A:L.70, A:M.111, A:A.114, A:V.122, A:V.122, A:V.122, A:F.123, A:F.124, A:L.142, A:I.143 Hydrogen bonds: A:L.33, A:R.113, A:F.123 Halogen bonds: A:S.150

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

EDO.2: 4 residues within 4Å: Chain A: H.18, L.19, S.22, S.85 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.18, A:S.22, A:S.85 Water bridges: A:L.19 EDO.3: 6 residues within 4Å: Chain A: C.112, L.153, S.154, H.157, F.158 Ligands: EDO.6 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:Y.115 EDO.4: 4 residues within 4Å: Chain A: Q.241, A.242, F.244, K.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.242, A:K.249 EDO.5: 4 residues within 4Å: Chain A: R.28, E.29, C.31, Y.76 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.29 EDO.6: 5 residues within 4Å: Chain A: R.42, N.116, A.117, S.154 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.42, A:R.42 EDO.7: 3 residues within 4Å: Chain A: Q.75, Y.76, E.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakajima, R. et al., Discovery of [1,2,4]Triazolo[1,5-a]pyridine Derivatives as Potent and Orally Bioavailable ROR gamma t Inverse Agonists. Acs Med.Chem.Lett. (2020)

Release Date

2020-03-04

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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