SMTL ID : 4wvs.1

Crystal structure of XIAP-BIR2 domain complexed with (S)-3-(4-methoxyphenyl)-2-((S)-2-((S)-1-((S)-2-((S)-2-(methylamino)propanamido)pent-4-ynoyl)pyrrolidine-2-carboxamido)-3-phenylpropanamido)propanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 x MAA- LPH- PRO- PHE- 4LZ: 3,11-DIFLUORO-6,8,13-TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN-13-IUM(Non-covalent)

MAA-LPH-PRO-PHE-4LZ.1: 15 residues within 4Å: Chain A: Q.64, V.65, K.73, L.74, K.75, N.76, W.77, E.78, D.81, E.86, R.89, H.90, F.91 Ligands: GOL.5, SO4.6 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Q.64, A:K.73, A:K.73, A:K.75, A:K.75, A:K.75, A:W.77, A:E.86, A:F.91 Hydrogen bonds: A:K.73, A:K.75, A:K.75, A:E.86, A:E.86 Water bridges: A:K.73 Salt bridges: A:K.73

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.67, C.70, H.87, C.94 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:H.87, A:C.94

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

SO4.3: 7 residues within 4Å: Chain A: G.20, H.21, A.69, C.70, N.93, C.94, F.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.93, A:F.95 SO4.4: 3 residues within 4Å: Chain A: Q.64, K.75, N.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.64, A:N.76 Salt bridges: A:K.75 SO4.6: 6 residues within 4Å: Chain A: R.23, C.70, G.72, F.91, N.93 Ligands: MAA-LPH-PRO-PHE-4LZ.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.93 Salt bridges: A:R.23

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Q.64, K.73 Ligands: MAA-LPH-PRO-PHE-4LZ.1, MAA-LPH-PRO-PHE-4LZ.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.73 Water bridges: A:Q.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seigal, B.A. et al., The Discovery of Macrocyclic XIAP Antagonists from a DNA-Programmed Chemistry Library, and Their Optimization To Give Lead Compounds with in Vivo Antitumor Activity. J.Med.Chem. (2015)

Release Date

2015-05-06

Peptides

E3 ubiquitin-protein ligase XIAP: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase XIAP

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