SMTL ID : 7f6m.1

Crystal structure of APC complexed with a peptide inhibitor MAI-516

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ANN- ALA- GLY- GLU- SER- LEU- TYR- GLU- NH2: MAI-516 inhibitor(Non-covalent)

ANN-ALA-GLY-GLU-SER-LEU-TYR-GLU-NH2.1: 24 residues within 4Å: Chain A: F.60, R.65, M.105, T.108, N.109, T.111, F.112, G.113, K.118, Q.144, V.145, S.148, R.151, N.152, W.155, R.156, S.192, W.195, N.196, A.199, N.243 Ligands: GOL.4, GOL.8, GOL.9 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.112, A:F.112, A:V.145, A:W.195, A:W.195, A:A.199 Hydrogen bonds: A:N.109, A:G.113, A:Q.144, A:R.151, A:N.152, A:N.152, A:N.196, A:N.196, A:N.196, A:N.243 Water bridges: A:R.151, A:W.155 Salt bridges: A:K.118, A:R.156 pi-Stacking: A:W.195

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain A: K.318 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.318 GOL.3: 3 residues within 4Å: Chain A: R.16, L.71, G.72 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.71 Water bridges: A:R.16, A:R.16, A:R.16 GOL.4: 8 residues within 4Å: Chain A: S.148, R.151, S.189 Ligands: ANN-ALA-GLY-GLU-SER-LEU-TYR-GLU-NH2.1, ANN-ALA-GLY-GLU-SER-LEU-TYR-GLU-NH2.1, ANN-ALA-GLY-GLU-SER-LEU-TYR-GLU-NH2.1, ANN-ALA-GLY-GLU-SER-LEU-TYR-GLU-NH2.1, ANN-ALA-GLY-GLU-SER-LEU-TYR-GLU-NH2.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.148, A:R.151, A:R.151 Water bridges: A:S.192, A:S.192 GOL.8: 5 residues within 4Å: Chain A: D.141, Q.144 Ligands: ANN-ALA-GLY-GLU-SER-LEU-TYR-GLU-NH2.1, ANN-ALA-GLY-GLU-SER-LEU-TYR-GLU-NH2.1, ANN-ALA-GLY-GLU-SER-LEU-TYR-GLU-NH2.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.141 Water bridges: A:K.183 GOL.9: 2 residues within 4Å: Chain A: W.155 Ligands: ANN-ALA-GLY-GLU-SER-LEU-TYR-GLU-NH2.1 No protein-ligand interaction detected (PLIP)

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

SO4.5: 4 residues within 4Å: Chain A: E.138, S.139, E.140, D.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.140, A:D.141 Water bridges: A:E.140 SO4.6: 2 residues within 4Å: Chain A: R.101, Y.102 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.101, A:R.101 Salt bridges: A:R.101

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

PEG.7: 4 residues within 4Å: Chain A: L.276, L.312, S.315, K.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.316 Water bridges: A:L.271 PEG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jie, Z. et al., Discovery of Efficient Adenomatous Polyposis Coli - Rho Guanine Nucleotide Exchange Factor 4 Inhibitors by Employing High Binding Affinity Tracer. To Be Published

Release Date

2022-06-29

Peptides

Adenomatous polyposis coli protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenomatous polyposis coli protein