SMTL ID : 9h1c.1

Crystal structure of Angiotensin-1 converting enzyme C-domain in complex with dual ACE/NEP inhibitor AD014

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.1: 10 residues within 4Å: Chain A: S.9, V.12, E.13, N.73, T.75, I.76, D.360, L.361, P.362, L.365 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.12, A:E.13 Hydrogen bonds: A:E.13, A:E.13, A:D.360

1 x 01: (2~{S},5~{R})-5-(3-hydroxyphenyl)-1-[2-[[(2~{S})-3-(4-hydroxyphenyl)-2-sulfanyl-propanoyl]amino]ethanoyl]pyrrolidine-2-carboxylic acid

01.2: 23 residues within 4Å: Chain A: Q.245, H.317, A.318, S.319, A.320, V.343, V.344, H.347, E.348, H.351, E.375, D.379, F.421, K.475, F.476, H.477, V.482, Y.484, Y.487, F.491 Ligands: BO3.4, EDO.9, ZN.11 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.344, A:F.421, A:F.476, A:Y.487 Hydrogen bonds: A:Q.245, A:H.317, A:A.318, A:H.347, A:D.379, A:H.477, A:Y.484, A:Y.487 Water bridges: A:K.418, A:K.475 Salt bridges: A:H.317, A:K.475, A:H.477

3 x BO3: BORIC ACID(Non-covalent)

BO3.3: 4 residues within 4Å: Chain A: F.257, D.404, I.408, W.566 No protein-ligand interaction detected (PLIP) BO3.4: 6 residues within 4Å: Chain A: Q.245, T.246, D.417, F.421, F.491 Ligands: 01.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.245, A:T.246, A:T.246, A:D.417, A:D.417 Water bridges: A:N.241 BO3.5: 10 residues within 4Å: Chain A: Y.251, S.262, P.388, L.397, E.400, H.406, N.409, F.410, K.413 Ligands: PGE.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.400, A:E.400 Water bridges: A:N.409

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 12 residues within 4Å: Chain A: Y.251, S.262, T.265, L.339, V.343, S.386, L.391, L.397, F.410, K.413, M.414 Ligands: BO3.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.413 Water bridges: A:S.248, A:D.417

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 8 residues within 4Å: Chain A: E.147, D.151, R.155, V.463, P.464, R.465, T.466, D.469 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.465, A:R.465, A:T.466, A:D.469

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain A: P.206, L.209, N.210, R.568, L.578 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.210, A:R.568, A:R.568 EDO.9: 7 residues within 4Å: Chain A: A.320, H.351, F.355, H.374, E.375, R.486 Ligands: 01.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.320

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.10: 5 residues within 4Å: Chain A: N.36, T.38, E.40, T.41, R.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.36, A:E.40

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 5 residues within 4Å: Chain A: H.347, H.351, E.375, Y.487 Ligands: 01.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.347, A:H.351, A:E.375

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 6 residues within 4Å: Chain A: W.146, R.150, W.449, W.450, R.453, D.471 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: Y.188, P.371, P.483, I.485, R.486 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cozier, G.E. et al., Design of Novel Mercapto-3-phenylpropanoyl Dipeptides as Dual Angiotensin-Converting Enzyme C-Domain-Selective/Neprilysin Inhibitors. J.Med.Chem. (2025)

Release Date

2025-04-16

Peptides

Angiotensin-converting enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Angiotensin-converting enzyme

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