SMTL ID : 9d17.1

Crystal structure of the catalytic region of human MASP-2 with specific inhibitor Compound S1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

1 x 01: 2-(2-amino-1H-1,3-benzimidazol-1-yl)-N-(5-ethylpyridin-2-yl)acetamide

01.1: 16 residues within 4Å: Chain A: F.167, P.244, Y.245, P.246, D.265, S.266, C.267, R.268, D.270, S.271, V.291, W.293, G.294, S.295, M.296, G.305 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.245, A:Y.245, A:V.291 Hydrogen bonds: A:S.271, A:G.294 Water bridges: A:G.269

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: S.198, R.201 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.198, A:S.198, A:R.201, A:R.201 GOL.3: 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

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 8 residues within 4Å: Chain A: R.77, G.85, G.86, Q.87, Y.225, V.226, D.227, K.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.227, A:K.264 Salt bridges: A:D.227 DMS.5: 9 residues within 4Å: Chain A: K.127, A.130, S.131, A.132, L.133, S.152, E.153, A.154, V.155 No protein-ligand interaction detected (PLIP) DMS.6: 4 residues within 4Å: Chain A: H.158, N.253, N.312, Y.313 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.158

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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