SMTL ID : 7s4e.1 (1 other biounit)

Crystal Structure of ligand ACBi1 in complex with bromodomain of human Smarca2 and pVHL:ElonginC:ElonginB complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: K.83, M.86, L.87, H.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.83 EDO.2: 3 residues within 4Å: Chain A: E.82, R.117, Q.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.117, A:Q.118 EDO.3: 2 residues within 4Å: Chain A: V.40 Ligands: 87A.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.59 EDO.5: 4 residues within 4Å: Chain A: Q.101 Chain B: I.58, H.59 Ligands: 87A.12 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.59, B:H.59, A:Q.101 EDO.7: 5 residues within 4Å: Chain B: R.31, T.73, D.75, R.110, Q.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.75, B:D.75, B:R.110, B:R.110 EDO.13: 3 residues within 4Å: Chain D: D.48, C.89, I.90 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.48, D:I.90, D:I.90 EDO.14: 4 residues within 4Å: Chain C: R.66, Y.67 Chain D: M.1, D.2 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.66, C:Y.67, C:Y.67, D:D.2, D:D.2

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: L.44, Y.53, P.60, V.61, N.91 Ligands: 87A.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.53, A:V.61, A:V.61, A:N.91 NA.9: 7 residues within 4Å: Chain B: V.15, N.16, S.17, R.18, F.40, H.64 Ligands: 87A.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.17, B:R.18, B:H.64 NA.10: 5 residues within 4Å: Chain B: P.20, S.21, H.59, S.60, Y.61 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:G.99 Hydrogen bonds: B:S.21 NA.11: 4 residues within 4Å: Chain B: P.103, V.104, Y.105 Chain C: Y.63 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.63, C:Y.63, B:Y.105 Water bridges: C:F.77

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain B: W.37, Q.45, P.46, Y.47 Ligands: 87A.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.47 PEG.8: 8 residues within 4Å: Chain B: D.75, G.76, E.83, P.103, Y.105, E.109, Q.113, P.141 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.75, B:E.109, B:Q.113

1 x 87A: N-(1-fluorocyclopropane-1-carbonyl)-3-methyl-L-valyl-(4R)-N-{[2-{2-[4-({4-[3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}methyl)phenoxy]ethoxy}-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-4-hydroxy-L-prolinamide(Non-covalent)

87A.12: 32 residues within 4Å: Chain A: V.40, F.41, L.44, P.45, L.50, Y.53, V.61, A.92, F.95, N.96, I.102 Chain B: N.16, R.18, F.25, P.35, W.37, F.40, Y.47, P.48, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Ligands: EDO.3, NA.4, EDO.5, PEG.6, NA.9 20 PLIP interactions: 7 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:L.44, A:L.50, A:F.95, B:W.37, B:F.40, B:I.58, B:I.58, B:Y.61, B:W.66 Hydrogen bonds: A:N.96, A:N.96, B:W.37, B:R.56, B:H.59, B:Y.61, B:Y.61, B:H.64 pi-Stacking: A:F.41, B:Y.47 Halogen bonds: A:N.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dixon, T. et al., Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry. Nat Commun (2022)

Release Date

2022-10-05

Peptides

Isoform Short of Probable global transcription activator SNF2L2: A
von Hippel-Lindau disease tumor suppressor: B
Elongin-C: C
Elongin-B: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isoform Short of Probable global transcription activator SNF2L2

von Hippel-Lindau disease tumor suppressor

Elongin-C

Elongin-B

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