SMTL ID : 9d4d.1

Crystal structure of the catalytic region of human MASP-2 with specific inhibitor Compound S3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

monomer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: E.69, P.70, C.72, L.111, Y.112, P.188, I.189, C.190, L.191 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.69, A:P.70, A:Y.112, A:I.189, A:L.191 GOL.2: 11 residues within 4Å: Chain A: P.91, G.92, D.93, F.94, P.95, Q.97, G.138, T.139, L.140, N.185, L.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.92, A:F.94, A:N.185 GOL.3: 9 residues within 4Å: Chain A: C.190, L.191, P.192, R.193, A.196, D.279, T.282, R.284, F.286 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.191, A:R.193, A:D.279, A:T.282 GOL.4: 6 residues within 4Å: Chain A: H.158, G.160, N.169, N.253, N.312, Y.313 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.169, A:N.169, A:N.253, A:N.312 Water bridges: A:H.158 GOL.5: 12 residues within 4Å: Chain A: T.162, A.165, G.166, F.167, D.168, P.246, R.247, G.248, S.249, T.251, M.254 Ligands: 01.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.162, A:F.167, A:D.168 GOL.6: 5 residues within 4Å: Chain A: P.145, H.146, Y.147, T.148, Q.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.145, A:Y.147 GOL.7: 7 residues within 4Å: Chain A: V.67, Y.112, D.113, N.114, W.115, K.179, I.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.114, A:W.115

1 x 01: 2-(2-amino-1H-1,3-benzimidazol-4-yl)-N-{4-[(pyridin-4-yl)methyl]phenyl}acetamide

01.8: 22 residues within 4Å: Chain A: H.121, G.166, F.167, P.244, Y.245, P.246, S.249, D.265, S.266, C.267, R.268, D.270, S.271, V.291, S.292, W.293, G.294, S.295, M.296, C.298, G.305 Ligands: GOL.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.167, A:Y.245, A:R.268, A:V.291 Hydrogen bonds: A:S.266, A:S.295, A:S.295 Water bridges: A:F.167 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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