SMTL ID : 7mph.2 (1 other biounit)

GRB2 SH2 Domain with Compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x ZLY: (4-{(10R,11E,14S,18S)-18-(2-amino-2-oxoethyl)-14-[(naphthalen-1-yl)methyl]-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl}phenyl)acetic acid(Non-covalent)

ZLY.1: 10 residues within 4Å: Chain A: R.29, S.39, Q.49, H.50, F.51, K.52, L.54, L.63, W.64 Ligands: EDO.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.49, A:H.50, A:F.51, A:L.54, A:W.64 Hydrogen bonds: A:S.39, A:S.39, A:H.50, A:K.52, A:K.52 Salt bridges: A:R.29 ZLY.8: 8 residues within 4Å: Chain B: R.29, S.39, H.50, F.51, K.52, L.54, L.63, W.64 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.50, B:F.51, B:K.52, B:L.54, B:W.64 Hydrogen bonds: B:S.39, B:H.50, B:K.52, B:L.63 Salt bridges: B:R.29, B:H.50 pi-Cation interactions: B:K.52 ZLY.12: 13 residues within 4Å: Chain A: R.55, G.57, A.58, G.59 Chain C: S.39, Q.49, H.50, F.51, K.52, L.54, L.63, W.64 Ligands: EDO.6 14 PLIP interactions: 1 interactions with chain A, 13 interactions with chain C Hydrophobic interactions: A:R.55, C:Q.49, C:H.50, C:F.51, C:K.52, C:K.52, C:L.54, C:W.64 Hydrogen bonds: C:S.39, C:H.50, C:K.52, C:K.52 Salt bridges: C:H.50, C:K.52

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

EDO.2: 7 residues within 4Å: Chain A: F.5, E.30 Chain B: W.3, F.5, L.71, N.72 Chain C: P.35 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Water bridges: B:L.71, B:L.71, B:N.72, C:R.55 Hydrogen bonds: A:E.30 EDO.3: 4 residues within 4Å: Chain A: W.64, V.65, V.66, H.78 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.65, A:V.66, A:H.78 Water bridges: A:W.64, A:W.64 EDO.4: 3 residues within 4Å: Chain A: R.21, H.22, D.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.21, A:D.23 EDO.5: 5 residues within 4Å: Chain A: L.54, R.55, D.56, F.62 Ligands: ZLY.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.55 EDO.6: 5 residues within 4Å: Chain A: G.36, R.55 Chain C: D.37, K.52 Ligands: ZLY.12 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.55, A:R.55, A:Y.61, C:K.52 EDO.13: 1 residues within 4Å: Chain C: R.92 No protein-ligand interaction detected (PLIP)

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

SO4.7: 2 residues within 4Å: Chain A: R.10, R.29 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.10, A:R.29 SO4.9: 3 residues within 4Å: Chain A: P.2 Chain B: P.9, R.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.10 Salt bridges: B:R.10 SO4.10: 2 residues within 4Å: Chain B: F.44, Q.87 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.87 SO4.11: 1 residues within 4Å: Chain B: K.12 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.12 Hydrogen bonds: A:E.95, A:E.95 SO4.14: 4 residues within 4Å: Chain B: K.60 Chain C: S.70, N.72, E.73 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.70, C:N.72 Salt bridges: B:K.60 SO4.15: 3 residues within 4Å: Chain B: N.69 Chain C: N.69, E.73 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.69, B:N.69 SO4.16: 6 residues within 4Å: Chain C: W.64, V.65, V.66, Y.77, H.78, R.85 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:L.63, C:W.64, C:V.65, C:V.66, C:V.66, C:Y.77 Water bridges: C:S.82, C:R.85 Salt bridges: C:H.78, C:R.85 SO4.17: 5 residues within 4Å: Chain A: S.70 Chain C: R.29, S.31, E.32, S.33 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.31, C:E.32, C:S.33, A:S.70, A:S.70 Water bridges: C:S.31 Salt bridges: C:R.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, T. et al., Synthesis and structural characterization of a monocarboxylic inhibitor for GRB2 SH2 domain. Bioorg.Med.Chem.Lett. (2021)

Release Date

2021-09-22

Peptides

Growth factor receptor-bound protein 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
B

Growth factor receptor-bound protein 2

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