SMTL ID : 9dtw.1

Co-crystal structure of the ternary complex of human FKBP12, QDPR and Compound 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: L.23, V.87, A.88, G.89, G.90, A.136, G.137, Y.151, K.155, P.183, L.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.87, A:G.89, A:G.137, A:K.155

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: T.145, P.146, G.147, M.148 Ligand excluded by PLIP

1 x 01: (2S)-N-[(2R)-1-({[(1R)-6-(4-[(4S)-5,6-dihydro[1,2,4]triazolo[1,5-a]pyrazin-7(8H)-yl]-6-{[(1S)-3-methyl-1-(1H-1,2,4-triazol-3-yl)butyl]amino}-1,3,5-triazin-2-yl)-6-azaspiro[2.5]octan-1-yl]methyl}amino)-4-(4-methoxyphenyl)-1-oxobutan-2-yl]-1-(3,3-dimethyl-2-oxopentanoyl)piperidine-2-carboxamide

01.3: 32 residues within 4Å: Chain A: Y.17, G.18, R.20, G.21, V.41, D.42, V.43, V.44, V.55, M.57, Q.64, V.87, A.88, G.89, L.107, K.110, Q.111, T.115 Chain B: Y.28, F.38, D.39, F.48, Q.55, E.56, V.57, I.58, W.61, Y.84, H.89, I.92, I.93, F.101 27 PLIP interactions: 12 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:Y.28, B:D.39, B:F.48, B:F.48, B:I.58, B:W.61, B:W.61, A:R.20, A:V.43, A:V.43, A:V.44, A:V.44, A:M.57, A:L.107 Hydrogen bonds: B:Y.28, B:Q.55, B:E.56, B:I.58, B:Y.84, A:G.18, A:G.21, A:D.42 Water bridges: A:Y.17, A:A.22, A:G.89, A:G.89, A:Q.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zandi, T.A. et al., Ternary complex DNA-encoded library screening uncovers FKBP molecular glues. To Be Published

Release Date

2025-10-08

Peptides

Dihydropteridine reductase: A
Peptidyl-prolyl cis-trans isomerase FKBP1A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydropteridine reductase

Peptidyl-prolyl cis-trans isomerase FKBP1A

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