SMTL ID : 9dty.1

Crystal structure of PRT3789 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

hetero-10-10-10-10-mer

Ligands

10 x 01: (4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide

01.1: 27 residues within 4Å: Chain A: V.37, F.38, L.41, P.42, L.47, Y.50, A.89, F.92, N.93 Chain B: N.15, R.17, F.24, P.34, W.36, F.39, Y.46, P.47, R.55, H.58, S.59, Y.60, H.63, W.65 Chain F: P.45, Y.46 Ligands: 01.3, ACT.4 17 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: B:W.36, B:Y.46, B:Y.46, B:Y.60, B:Y.60, B:W.65, A:L.41, F:Y.46 Hydrogen bonds: B:Y.46, B:R.55, B:H.58, B:Y.60, B:W.65, A:N.93, A:N.93 Water bridges: B:Y.60 pi-Stacking: A:F.38 01.3: 22 residues within 4Å: Chain E: V.37, F.38, L.47, V.58, D.59, L.85, F.92 Chain F: N.15, R.17, P.34, W.36, F.39, Y.46, P.47, R.55, I.57, H.58, S.59, Y.60, H.63, W.65 Ligands: 01.1 17 PLIP interactions: 12 interactions with chain F, 5 interactions with chain E Hydrophobic interactions: F:R.17, F:F.39, F:I.57, F:Y.60, F:W.65, E:F.38, E:F.38, E:D.59 Hydrogen bonds: F:R.17, F:R.55, F:H.58, F:Y.60, F:H.63, F:W.65 pi-Stacking: F:Y.46 Water bridges: E:Y.50, E:Y.50 01.5: 22 residues within 4Å: Chain I: V.37, F.38, Q.40, L.41, P.42, V.58, D.59 Chain J: N.15, R.17, P.34, W.36, F.39, Y.46, P.47, R.55, I.57, H.58, S.59, Y.60, H.63, W.65 Ligands: 01.7 16 PLIP interactions: 12 interactions with chain J, 4 interactions with chain I Hydrophobic interactions: J:W.36, J:Y.46, J:Y.46, J:I.57, J:Y.60, J:W.65, I:V.37, I:F.38, I:L.41, I:D.59 Hydrogen bonds: J:R.55, J:H.58, J:S.59, J:Y.60, J:H.63 pi-Stacking: J:Y.60 01.6: 16 residues within 4Å: Chain N: N.15, P.34, W.36, F.39, Y.46, P.47, R.55, I.57, H.58, S.59, Y.60, H.63, W.65 Chain Q: D.102, S.103 Ligands: 01.9 11 PLIP interactions: 10 interactions with chain N, 1 interactions with chain Q Hydrophobic interactions: N:F.39, N:Y.46, N:Y.46, N:I.57, N:W.65, Q:D.102 Hydrogen bonds: N:Y.46, N:R.55, N:H.58, N:Y.60, N:W.65 01.7: 27 residues within 4Å: Chain J: P.45, Y.46, P.47 Chain M: V.37, F.38, Q.40, L.41, L.47, Y.50, A.89, F.92, N.93 Chain R: N.15, R.17, F.24, P.34, W.36, F.39, Y.46, P.47, R.55, I.57, S.59, Y.60, H.63, W.65 Ligands: 01.5 15 PLIP interactions: 11 interactions with chain R, 3 interactions with chain M, 1 interactions with chain J Hydrophobic interactions: R:W.36, R:W.36, R:I.57, R:Y.60, R:W.65, M:L.41, J:Y.46 Hydrogen bonds: R:Y.46, R:R.55, R:S.59, R:Y.60, M:N.93 pi-Stacking: R:Y.46, R:Y.60, M:F.38 01.9: 27 residues within 4Å: Chain N: P.45, Y.46, P.47 Chain U: V.37, F.38, L.41, P.42, L.47, Y.50, V.58, A.89, N.93, I.99 Chain V: N.15, R.17, F.24, W.36, F.39, Y.46, P.47, R.55, H.58, S.59, Y.60, H.63, W.65 Ligands: 01.6 17 PLIP interactions: 11 interactions with chain V, 5 interactions with chain U, 1 interactions with chain N Hydrophobic interactions: V:W.36, V:Y.60, V:W.65, U:L.41, N:Y.46 Hydrogen bonds: V:R.17, V:R.55, V:H.58, V:S.59, V:Y.60, V:H.63, U:Y.50, U:N.93, U:N.93 Water bridges: V:N.15 pi-Stacking: V:Y.46, U:F.38 01.11: 29 residues within 4Å: Chain 7: P.45, Y.46 Chain Y: V.37, F.38, Q.40, L.41, P.42, L.47, Y.50, V.58, D.59, A.89, F.92, N.93 Chain Z: N.15, S.16, F.24, P.34, W.36, F.39, Y.46, P.47, R.55, H.58, S.59, Y.60, H.63, W.65 Ligands: 01.15 20 PLIP interactions: 6 interactions with chain Y, 2 interactions with chain 7, 12 interactions with chain Z Hydrophobic interactions: Y:L.41, Y:L.47, Y:D.59, 7:Y.46, 7:Y.46, Z:Y.60, Z:Y.60, Z:W.65 Hydrogen bonds: Y:N.93, Y:N.93, Z:Y.46, Z:R.55, Z:H.58, Z:S.59, Z:Y.60 pi-Stacking: Y:F.38, Z:Y.46 Water bridges: Z:N.15, Z:N.15, Z:Y.60 01.13: 28 residues within 4Å: Chain 2: V.37, F.38, L.41, L.47, Y.50, V.58, L.85, A.89, F.92, N.93 Chain 3: N.15, R.17, F.24, P.34, W.36, F.39, Y.46, P.47, R.55, I.57, H.58, S.59, Y.60, H.63, W.65 Ligands: 01.16 Chain b: P.45, Y.46 17 PLIP interactions: 12 interactions with chain 3, 4 interactions with chain 2, 1 interactions with chain b Hydrophobic interactions: 3:W.36, 3:Y.46, 3:Y.46, 3:Y.60, 3:W.65, 2:L.41, b:Y.46 Hydrogen bonds: 3:N.15, 3:R.55, 3:H.58, 3:S.59, 3:Y.60, 3:H.63, 2:Y.50, 2:N.93, 2:N.93 pi-Stacking: 3:Y.60 01.15: 25 residues within 4Å: Chain 6: V.37, F.38, L.41, Y.50, V.58, D.59, L.85, A.89, N.93, I.99 Chain 7: N.15, P.34, W.36, F.39, Y.46, P.47, R.55, I.57, H.58, S.59, Y.60, H.63, W.65 Chain Z: H.58 Ligands: 01.11 16 PLIP interactions: 6 interactions with chain 6, 10 interactions with chain 7 Hydrophobic interactions: 6:V.37, 6:L.41, 6:D.59, 6:L.85, 7:Y.46, 7:Y.46, 7:Y.60, 7:W.65 Hydrogen bonds: 6:N.93, 7:N.15, 7:R.55, 7:H.58, 7:Y.60, 7:H.63, 7:W.65 pi-Stacking: 6:F.38 01.16: 24 residues within 4Å: Chain 3: H.58 Ligands: 01.13 Chain a: P.42, E.46, L.47, F.92, N.93, L.94 Chain b: N.15, S.16, R.17, F.24, P.34, W.36, F.39, Y.46, P.47, R.55, I.57, H.58, S.59, Y.60, H.63, W.65 13 PLIP interactions: 4 interactions with chain a, 9 interactions with chain b Hydrophobic interactions: a:F.92, a:N.93, a:L.94, b:I.57, b:Y.60, b:W.65 Salt bridges: a:E.46 Hydrogen bonds: b:Y.46, b:R.55, b:H.58, b:S.59, b:Y.60 pi-Stacking: b:Y.46

5 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 8 residues within 4Å: Chain C: R.66, S.70, S.71, T.72, E.73 Chain J: G.52, T.53, G.54 10 PLIP interactions: 3 interactions with chain J, 7 interactions with chain C Hydrophobic interactions: J:T.53 Hydrogen bonds: J:G.54, J:G.54, C:R.66, C:R.66, C:T.72, C:T.72, C:E.73 Salt bridges: C:R.66, C:R.66 CIT.8: 8 residues within 4Å: Chain 3: G.52, T.53, G.54 Chain S: R.66, S.70, S.71, T.72, E.73 4 PLIP interactions: 1 interactions with chain 3, 3 interactions with chain S Hydrogen bonds: 3:G.54, S:T.72, S:E.73 Salt bridges: S:R.66 CIT.10: 6 residues within 4Å: Chain W: R.66, S.70, S.71, T.72, E.73 Chain X: M.1 5 PLIP interactions: 5 interactions with chain W Hydrogen bonds: W:R.66, W:S.71, W:T.72, W:E.73 Salt bridges: W:R.66 CIT.12: 8 residues within 4Å: Chain 0: R.66, S.70, S.71, T.72, E.73 Chain V: G.52, T.53, G.54 5 PLIP interactions: 4 interactions with chain 0, 1 interactions with chain V Hydrogen bonds: 0:S.71, 0:T.72, 0:E.73, V:G.54 Salt bridges: 0:R.66 CIT.14: 7 residues within 4Å: Chain 4: R.66, S.70, S.71, T.72 Chain R: G.52, T.53, G.54 7 PLIP interactions: 2 interactions with chain R, 5 interactions with chain 4 Hydrogen bonds: R:G.52, R:G.54, 4:R.66, 4:R.66, 4:S.71, 4:T.72 Salt bridges: 4:R.66

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: L.47 Chain F: H.58 Ligands: 01.1 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:H.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hulse, M. et al., PRT3789 is a First-in-Human SMARCA2-Selective Degrader that Induces Synthetic Lethality in SMARCA4-Mutated Cancers. Cancer Res. (2025)

Release Date

2025-10-01

Peptides

Isoform Short of Probable global transcription activator SNF2L2: AEIMQUY26a
von Hippel-Lindau disease tumor suppressor: BFJNRVZ37b
Elongin-C: CGKOSW048c
Elongin-B: DHLPTX159d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

M
M

Q
Q

U
U

Y
Y

2
c

6
g

a
k

B
B

F
F

J
J

N
N

R
R

V
V

Z
Z

3
d

7
h

b
l

C
C

G
G

K
K

O
O

S
S

W
W

0
a

4
e

8
i

c
m

D
D

H
H

L
L

P
P

T
T

X
X

1
b

5
f

9
j

d
n

Isoform Short of Probable global transcription activator SNF2L2

von Hippel-Lindau disease tumor suppressor

Elongin-C

Elongin-B

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