SMTL ID : 9d3y.1

Crystal structure of the catalytic region of human MASP-2 with specific inhibitor Compound S2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: R.77, G.86, Q.87, Y.225, V.226, D.227, K.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.225, A:D.227, A:D.227, A:K.264 GOL.2: 9 residues within 4Å: Chain A: E.69, P.70, C.72, L.111, Y.112, P.188, I.189, C.190, L.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.70, A:Y.112, A:I.189, A:L.191 GOL.3: 9 residues within 4Å: Chain A: T.162, A.165, G.166, F.167, D.168, G.248, S.249, T.251, M.254 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.162, A:F.167, A:D.168 Water bridges: A:T.162, A:S.249 GOL.4: 12 residues within 4Å: Chain A: K.90, P.91, G.92, D.93, F.94, P.95, Q.97, G.138, T.139, L.140, N.185, L.223 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.92, A:F.94, A:N.185, A:N.185 Water bridges: A:F.94, A:F.94 GOL.5: 10 residues within 4Å: Chain A: Q.126, K.127, A.130, S.131, A.132, L.133, S.152, E.153, A.154, V.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.126, A:S.152, A:E.153 GOL.6: 5 residues within 4Å: Chain A: H.158, N.169, N.253, N.312, Y.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.169, A:N.253, A:N.312

1 x 01: (2S)-N-[2-(2-amino-1H-1,3-benzimidazol-5-yl)ethyl]-1-[(2R,4S)-4-phenylpiperidine-2-carbonyl]azetidine-2-carboxamide

01.7: 28 residues within 4Å: Chain A: H.121, G.166, F.167, Y.240, P.244, Y.245, P.246, S.249, D.265, S.266, C.267, R.268, G.269, D.270, S.271, V.291, S.292, W.293, G.294, S.295, M.296, N.297, C.298, G.299, Q.303, Y.304, G.305, V.306 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.167, A:Y.245, A:Y.245, A:P.246 Hydrogen bonds: A:Y.240, A:S.266, A:R.268, A:S.271, A:S.292, A:G.294, A:G.294, A:S.295, A:S.295 Salt bridges: A:D.265 pi-Stacking: A:F.167, A:W.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakhla, M.C. et al., Small molecule inhibitors of mannan-binding lectin-associated serine Proteases-2 and-3. Eur.J.Med.Chem. (2025)

Release Date

2025-04-16

Peptides

Mannan-binding lectin serine protease 2 B chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mannan-binding lectin serine protease 2 B chain

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