SMTL ID : 9h1b.1

Crystal structure of Angiotensin-1 converting enzyme N-domain in complex with dual ACE/NEP inhibitor AD015

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- FUC: 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-FUC.1: 10 residues within 4Å: Chain A: E.403, N.416, D.417, T.418, D.421, Y.521, E.522, G.523, P.524, Q.527 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.4: 6 residues within 4Å: Chain B: E.403, N.416, E.522, G.523, P.524, Q.527 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.522

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 10 residues within 4Å: Chain A: V.477, T.478, N.480, T.482, H.483, L.603 Chain B: R.245, P.595, E.596 Ligands: EDO.13 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:N.480, A:N.480 Hydrogen bonds: B:R.245, B:E.596, A:T.482, A:T.482 NAG-FUC.5: 9 residues within 4Å: Chain A: R.245, P.595, E.596 Chain B: V.477, T.478, N.480, T.482, H.483, L.603 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.478, B:T.478, B:T.482, B:T.482, A:R.245, A:R.245 Water bridges: B:H.483, B:N.480

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 7 residues within 4Å: Chain B: N.45, T.47, E.49, N.50, R.53, D.324, R.326 No protein-ligand interaction detected (PLIP)

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

NAG.6: 7 residues within 4Å: Chain A: N.45, T.47, E.49, N.50, R.53, D.324, R.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.45, A:T.47, A:E.49, A:N.50

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 15 residues within 4Å: Chain A: Q.444, W.445, G.448, R.453, T.454, D.462, Y.465, L.466 Chain B: W.445, R.453, T.454, D.462, Y.465, L.466 Ligands: PEG.29 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.453, B:R.453, A:T.454, A:T.454 Water bridges: B:G.448, B:R.453, B:Y.465, A:V.449

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.8: 5 residues within 4Å: Chain A: R.199, E.208, W.447, G.448, S.451 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.447 Water bridges: A:R.199 Salt bridges: A:R.199 ACY.23: 5 residues within 4Å: Chain B: E.513, D.566, Q.568, P.569, K.572 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.568 Salt bridges: B:K.572 ACY.28: 5 residues within 4Å: Chain B: R.199, E.208, W.447, G.448, S.451 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.199, B:W.447, B:G.448, B:R.453 Salt bridges: B:R.199

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

EDO.9: 8 residues within 4Å: Chain A: A.334, H.365, Y.369, H.388, E.389, R.500 Ligands: PGE.10, 01.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.334, A:H.388 EDO.11: 8 residues within 4Å: Chain A: R.199, S.200, S.204, P.205, T.206, F.207, E.208, D.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.204, A:F.207, A:E.208 EDO.12: 4 residues within 4Å: Chain A: R.96, D.189, G.190, F.191 No protein-ligand interaction detected (PLIP) EDO.13: 5 residues within 4Å: Chain A: E.161, V.477, T.478, L.603 Ligands: NAG-FUC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.478 Water bridges: A:E.161, A:E.161 EDO.24: 8 residues within 4Å: Chain B: Y.24, F.64, A.65, W.68, G.69, V.95, T.97, L.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.69, B:V.95 Water bridges: B:Y.24 EDO.25: 4 residues within 4Å: Chain B: W.201, R.381, P.385 Ligands: PEG.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.381 EDO.26: 7 residues within 4Å: Chain B: L.32, S.35, V.36, S.39, W.335, Y.338 Ligands: EDO.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.39, B:S.39 EDO.27: 9 residues within 4Å: Chain B: V.36, S.39, S.333, A.334, W.335, Y.369 Ligands: PEG.22, EDO.26, 01.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.334 Water bridges: B:S.39, B:D.336

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

PGE.10: 10 residues within 4Å: Chain A: L.32, S.35, V.36, S.39, S.333, A.334, W.335, Y.338 Ligands: EDO.9, 01.16 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.14: 5 residues within 4Å: Chain A: H.361, H.365, E.389, Y.501 Ligands: 01.16 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.361, A:H.365, A:E.389 ZN.30: 5 residues within 4Å: Chain B: H.361, H.365, E.389, Y.501 Ligands: 01.32 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.361, B:H.365, B:E.389

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

CL.15: 6 residues within 4Å: Chain A: W.201, Y.202, P.385, P.497, I.499, R.500 Ligand excluded by PLIP CL.31: 6 residues within 4Å: Chain B: W.201, Y.202, P.385, P.497, I.499, R.500 Ligand excluded by PLIP

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

01.16: 25 residues within 4Å: Chain A: Q.259, H.331, A.332, S.333, A.334, D.354, S.357, T.358, H.361, E.362, H.365, E.389, D.393, E.431, F.435, K.489, F.490, H.491, T.496, Y.498, Y.501, F.505 Ligands: EDO.9, PGE.10, ZN.14 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.361, A:F.435, A:F.490, A:Y.501 Hydrogen bonds: A:Q.259, A:A.332, A:H.491 Water bridges: A:H.331, A:K.489, A:K.489 Salt bridges: A:H.331, A:K.489, A:H.491 01.32: 25 residues within 4Å: Chain B: Q.259, H.331, A.332, S.333, A.334, D.354, S.357, T.358, H.361, E.362, H.365, E.389, D.393, E.431, F.435, K.489, F.490, H.491, T.496, Y.498, Y.501, F.505 Ligands: PEG.22, EDO.27, ZN.30 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:H.361, B:F.435, B:F.490, B:Y.501, B:F.505 Hydrogen bonds: B:Q.259, B:A.332 Water bridges: B:H.331, B:K.489, B:K.489 Salt bridges: B:H.331, B:K.489, B:H.491

3 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 4 residues within 4Å: Chain A: S.260, E.262, N.263, D.354 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.262, H2O.12 MG.33: 4 residues within 4Å: Chain B: E.262, N.263, T.352, D.354 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.262, B:E.262, B:D.354, H2O.26, H2O.28 MG.34: 4 residues within 4Å: Chain B: D.255, S.260, E.262, N.263 No protein-ligand interaction detected (PLIP)

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 10 residues within 4Å: Chain B: F.228, R.231, A.232, R.235, R.236, M.267, V.268, V.269, P.270, N.588 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.228, B:A.232, B:R.235 PEG.20: 2 residues within 4Å: Chain B: R.295 Ligands: PE8.19 No protein-ligand interaction detected (PLIP) PEG.21: 6 residues within 4Å: Chain B: W.80, Q.81, R.96, D.189, G.190, F.191 No protein-ligand interaction detected (PLIP) PEG.22: 13 residues within 4Å: Chain B: Y.338, H.365, Y.369, Y.372, R.380, R.381, G.382, H.388, E.389, R.500 Ligands: EDO.25, EDO.27, 01.32 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.382 PEG.29: 9 residues within 4Å: Chain A: Y.465 Chain B: W.445, G.448, R.453, T.454, D.462, Y.465, L.466 Ligands: PG4.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.453, B:R.453, B:Y.465 Water bridges: B:Q.444, B:G.448, B:R.453, B:Y.465

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.19: 10 residues within 4Å: Chain B: Q.286, G.287, W.288, T.291, H.292, R.295, V.296, E.299, I.408 Ligands: PEG.20 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.299

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, soluble form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Angiotensin-converting enzyme, soluble form

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