SMTL ID : 8hck.1

NMR fragment-based screening against the two PDZ do-mains of MDA-9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x P1Z: 4-BUTYL-1,2-DIPHENYL-PYRAZOLIDINE-3,5-DIONE(Non-covalent)

P1Z.1: 9 residues within 4Å: Chain A: K.14, I.15, G.16, L.17, R.18, Q.32, H.65, L.68, K.69 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.14, A:I.15, A:Q.32, A:L.68 Hydrogen bonds: A:I.15, A:G.16, A:Q.32 P1Z.6: 9 residues within 4Å: Chain B: K.14, I.15, G.16, L.17, R.18, Q.32, H.65, L.68, K.69 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.14, B:I.15, B:Q.32, B:L.68 Hydrogen bonds: B:I.15, B:G.16, B:Q.32

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

SO4.2: 5 residues within 4Å: Chain A: V.5, I.6, V.40 Chain B: I.6, K.75 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.75 Hydrogen bonds: A:I.6, A:I.6 SO4.3: 3 residues within 4Å: Chain A: I.22, D.23, F.27 No protein-ligand interaction detected (PLIP) SO4.7: 5 residues within 4Å: Chain A: I.6, K.75 Chain B: V.5, I.6, V.40 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.75 Hydrogen bonds: B:I.6, B:I.6 SO4.8: 3 residues within 4Å: Chain B: I.22, D.23, F.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.23

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: S.21, S.60, S.61, D.62 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.21, A:S.21, A:S.60, A:S.61, A:D.62 GOL.5: 2 residues within 4Å: Chain A: M.1, H.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.1, A:H.2 GOL.9: 4 residues within 4Å: Chain B: S.21, S.60, S.61, D.62 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.21, B:S.21, B:S.60, B:S.61, B:D.62 GOL.10: 2 residues within 4Å: Chain B: M.1, H.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.1, B:H.2, B:H.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, H. et al., Inhibitors against Two PDZ Domains of MDA-9 Suppressed Migration of Breast Cancer Cells. Int J Mol Sci (2023)

Release Date

2023-11-08

Peptides

Syntenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Syntenin-1