SMTL ID : 9du1.1

Co-crystal structure of the ternary complex of human FKBP12, BRD9 bromo domain and Compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-4-4-mer

Ligands

4 x 01: 4-[4-{cyclopropyl[(1-methyl-1H-pyrazol-4-yl)methyl]amino}-6-({1-[(2R)-2-{[(2S)-1-(3,3-dimethyl-2-oxopentanoyl)piperidine-2-carbonyl]amino}-4-(4-methoxyphenyl)butanoyl]piperidin-4-yl}amino)-1,3,5-triazin-2-yl]-N-ethylpiperazine-1-carboxamide

01.1: 28 residues within 4Å: Chain B: Y.28, F.38, D.39, F.48, K.49, Q.55, E.56, V.57, I.58, W.61, Y.84, H.89, I.92, I.93, F.101 Chain F: F.36, F.37, V.41, I.45, A.46, P.47, G.48, A.88, Y.91, N.92, R.93, Y.98 Ligands: GOL.3 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain F Hydrophobic interactions: B:Y.28, B:F.38, B:D.39, B:F.48, B:V.57, B:I.58, B:W.61, B:H.89, B:I.92, B:I.93, F:F.37, F:A.88, F:Y.98 Hydrogen bonds: B:E.56, B:I.58, B:Y.84, F:F.36, F:N.92 Water bridges: B:V.57, F:R.93 pi-Cation interactions: F:R.93 01.2: 27 residues within 4Å: Chain D: Y.28, F.38, D.39, F.48, K.49, Q.55, E.56, V.57, I.58, W.61, Y.84, H.89, I.92, F.101 Chain E: F.36, F.37, V.41, I.45, A.46, P.47, G.48, M.51, A.88, Y.91, N.92, R.93, Y.98 20 PLIP interactions: 8 interactions with chain E, 12 interactions with chain D Hydrophobic interactions: E:F.37, E:A.88, E:Y.98, D:Y.28, D:D.39, D:F.48, D:I.58, D:W.61, D:H.89, D:I.92 Hydrogen bonds: E:F.36, E:N.92, E:Y.98, D:Y.28, D:D.39, D:E.56, D:I.58, D:Y.84 Water bridges: E:R.93 pi-Cation interactions: E:R.93 01.4: 11 residues within 4Å: Chain G: F.36, F.37, V.41, I.45, P.47, G.48, A.88, Y.91, N.92, R.93, Y.98 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:F.37, G:P.47, G:A.88, G:Y.98 Hydrogen bonds: G:F.36, G:N.92 Water bridges: G:I.45 pi-Cation interactions: G:R.93 01.5: 13 residues within 4Å: Chain H: F.36, F.37, V.41, I.45, A.46, P.47, G.48, M.51, A.88, Y.91, N.92, R.93, Y.98 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:F.37, H:P.47, H:A.88, H:Y.98 Hydrogen bonds: H:F.36, H:Y.91, H:N.92 pi-Cation interactions: H:R.93

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.15 Chain B: H.89 Chain F: I.52, T.90, Y.91 Ligands: 01.1 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:T.90, A:R.15 Water bridges: F:R.93

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

Peptidyl-prolyl cis-trans isomerase FKBP1A: ABCD
Bromodomain-containing protein 9: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Peptidyl-prolyl cis-trans isomerase FKBP1A

Bromodomain-containing protein 9

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