SMTL ID : 6fmf.1

Neuropilin-1 b1 domain in complex with EG01377; 2.8 Angstrom structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

monomer

Ligands

1 x DUE: (2~{S})-2-[[3-[[5-[4-(aminomethyl)phenyl]-1-benzofuran-7-yl]sulfonylamino]thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid(Non-covalent)

DUE.1: 15 residues within 4Å: Chain A: Y.28, S.29, T.30, N.31, W.32, T.47, D.51, S.77, E.79, T.80, K.82, Y.84, G.145, I.146 Ligands: TFA.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.28, A:W.32, A:E.79, A:E.79 Hydrogen bonds: A:S.29, A:S.77, A:E.79, A:Y.84, A:I.146 Salt bridges: A:D.51, A:K.82

1 x TFA: trifluoroacetic acid(Non-covalent)

TFA.2: 5 residues within 4Å: Chain A: Q.27, Y.28, S.29, T.30 Ligands: DUE.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.30 Halogen bonds: A:Q.27, A:Y.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Powell, J. et al., Small Molecule Neuropilin-1 Antagonists Combine Antiangiogenic and Antitumor Activity with Immune Modulation through Reduction of Transforming Growth Factor Beta (TGF beta ) Production in Regulatory T-Cells. J. Med. Chem. (2018)

Release Date

2018-10-17

Peptides

Neuropilin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neuropilin-1

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