SMTL ID : 9f6b.1

Human neuropilin-1 in a complex with a quinoline based antagonists

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

2 x 01: (2~{S})-2-[[3-[[6-[3-(aminomethyl)phenyl]quinolin-8-yl]sulfonylamino]thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid

01.1: 17 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 Chain B: K.5, M.7, Y.153 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.28, A:W.32, A:E.79, B:Y.153 Hydrogen bonds: A:S.29, A:N.31, A:S.77, A:T.80, A:I.146 Water bridges: A:Y.28, A:W.32, A:T.47, A:D.51, A:S.77, A:E.79, B:K.5, B:K.5 Salt bridges: A:D.51 01.2: 14 residues within 4Å: Chain B: 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 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.28, B:W.32, B:E.79 Hydrogen bonds: B:S.29, B:N.31, B:S.77, B:T.80, B:I.146 Water bridges: B:Y.28, B:W.32, B:D.51, B:S.77 Salt bridges: B:D.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mota, F. et al., Quinoline based neuropilin-1 antagonists exhibit a pure antagonist profile and block pain transmission. To Be Published

Release Date

2025-05-14

Peptides

Neuropilin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Neuropilin-1

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