SMTL ID : 8pbo.1 (1 other biounit)

Deep interactome learning for generative drug design

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x Y5I: 3-[2-fluoranyl-4-[3-[2-fluoranyl-4-(5-methyl-1,3,4-thiadiazol-2-yl)phenoxy]propoxy]phenyl]propanoic acid

Y5I.1: 27 residues within 4Å: Chain A: L.53, E.57, F.62, R.78, I.79, G.82, C.83, Q.84, R.86, S.87, H.121, I.124, Y.125, L.128, M.132, V.137, L.138, I.139, M.146, L.151, F.161, M.162, K.165, H.247, L.251, L.267, Y.271 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.125, A:L.128, A:V.137, A:I.139 Water bridges: A:Q.84 Salt bridges: A:H.121, A:H.247

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: I.34, L.35, P.44, V.46, N.133, D.135, F.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.133 GOL.3: 5 residues within 4Å: Chain A: L.199, N.200, V.201, K.202, P.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.201, A:K.202 GOL.4: 7 residues within 4Å: Chain A: R.10, K.14, S.180, Q.218, L.221, N.222 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.180, A:Q.218 Water bridges: A:R.10

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

SO4.5: 4 residues within 4Å: Chain A: R.10, K.14, L.221 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.10, A:K.14 SO4.6: 2 residues within 4Å: Chain A: S.227, Q.228 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.227, A:S.227, A:Q.228, A:Q.228 Salt bridges: A:K.220 SO4.7: 3 residues within 4Å: Chain A: R.32, T.36, K.38 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.32 SO4.8: 4 residues within 4Å: Chain A: H.223, P.224, E.225, S.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.223, A:E.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atz, K. et al., Prospective de novo drug design with deep interactome learning. Nat Commun (2024)

Release Date

2024-05-15

Peptides

Peroxisome proliferator-activated receptor gamma: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peroxisome proliferator-activated receptor gamma

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