SMTL ID : 9h1a.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 7 residues within 4Å: Chain A: N.45, T.47, E.49, N.50, R.53, D.324, R.326 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain B: E.403, N.416, E.522, G.523, P.524, Q.527 Ligands: FUC.18, BMA.19 No protein-ligand interaction detected (PLIP)

1 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.2: 6 residues within 4Å: Chain A: E.403, N.416, E.522, G.523, P.524, Q.527 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.522

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

NAG-FUC.4: 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 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.245, A:E.596, A:E.596, B:T.478, B:N.480 Water bridges: B:N.480, B:N.480, B:T.478, B:H.483

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

NAG.5: 6 residues within 4Å: Chain A: N.480, T.482, H.483 Chain B: R.245, P.595, E.596 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.245, B:R.245, B:E.596, A:T.482 NAG.17: 7 residues within 4Å: Chain B: N.45, T.47, E.49, N.50, R.53, D.324, R.326 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.45, B:T.47, B:E.49, B:E.49, B:N.50, B:R.53

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: H.361, H.365, E.389, Y.501 Ligands: 01.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.361, A:H.365, A:E.389 ZN.20: 5 residues within 4Å: Chain B: H.361, H.365, E.389, Y.501 Ligands: 01.21 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.361, B:H.365, B:E.389

2 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

01.7: 24 residues within 4Å: Chain A: Q.259, H.331, A.332, S.333, A.334, S.357, T.358, H.361, E.362, H.365, E.389, D.393, K.432, F.435, K.489, F.490, H.491, N.494, T.496, Y.498, Y.501, F.505 Ligands: ZN.6, PGE.16 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.435, A:F.490, A:T.496, A:Y.501, A:F.505 Hydrogen bonds: A:Q.259, A:H.331, A:A.332, A:H.361, A:D.393, A:H.491, A:Y.498, A:Y.501 Water bridges: A:K.432 Salt bridges: A:H.331, A:K.489, A:H.491 01.21: 24 residues within 4Å: Chain B: Q.259, H.331, A.332, S.333, A.334, S.357, T.358, H.361, E.362, H.365, E.389, D.393, K.432, F.435, K.489, F.490, H.491, T.496, Y.498, R.500, Y.501, F.505 Ligands: ZN.20, EDO.26 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.435, B:F.490, B:T.496, B:Y.501, B:F.505 Hydrogen bonds: B:Q.259, B:H.331, B:A.332, B:H.361, B:D.393, B:H.491, B:Y.498, B:Y.501 Water bridges: B:H.361, B:E.431, B:K.489, B:K.489 Salt bridges: B:H.331, B:K.489, B:H.491

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

CL.8: 6 residues within 4Å: Chain A: W.201, Y.202, P.385, P.497, I.499, R.500 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain B: W.201, Y.202, P.385, P.497, I.499, R.500 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain A: N.263, D.354 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.354, H2O.2, H2O.9 MG.23: 4 residues within 4Å: Chain B: S.260, E.262, N.263, D.354 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.262, B:D.354, H2O.18, H2O.21, H2O.26

1 x XPE: 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL(Non-covalent)

XPE.10: 10 residues within 4Å: Chain A: Q.286, G.287, W.288, Q.289, T.291, H.292, R.295, V.296, E.299, I.408 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.295

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

ACY.11: 6 residues within 4Å: Chain A: R.199, E.208, W.447, G.448, S.451 Ligands: PG4.12 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.199, A:G.448 Salt bridges: A:R.199 ACY.24: 5 residues within 4Å: Chain B: R.199, E.208, W.447, G.448, S.451 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.199, B:G.448 Salt bridges: B:R.199

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

PG4.12: 18 residues within 4Å: Chain A: Q.444, W.445, G.448, S.451, R.453, T.454, D.462, Y.465, L.466 Chain B: Q.444, W.445, G.448, R.453, T.454, D.462, Y.465, L.466 Ligands: ACY.11 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.453 Water bridges: B:Q.444, B:G.448, B:R.453, B:R.453, A:W.447, A:G.448, A:G.448

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

EDO.13: 4 residues within 4Å: Chain A: W.201, R.381, P.385 Ligands: PGE.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.381 EDO.14: 5 residues within 4Å: Chain A: F.228, R.231, A.232, R.235, V.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.228, A:R.235, A:V.268 EDO.25: 8 residues within 4Å: Chain B: R.199, S.200, S.204, P.205, T.206, F.207, E.208, D.209 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.204, B:F.207, B:E.208 Water bridges: B:P.205, B:T.206 EDO.26: 6 residues within 4Å: Chain B: H.365, Y.369, H.388, E.389, R.500 Ligands: 01.21 No protein-ligand interaction detected (PLIP)

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

PEG.15: 5 residues within 4Å: Chain A: W.80, R.96, D.189, G.190, F.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96

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

PGE.16: 14 residues within 4Å: Chain A: S.333, A.334, Y.338, H.365, Y.369, Y.372, R.380, R.381, G.382, H.388, E.389, R.500 Ligands: 01.7, EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.334, A:R.381

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.18: 6 residues within 4Å: Chain B: N.416, D.417, T.418, D.421 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP)

1 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.19: 2 residues within 4Å: Chain B: E.522 Ligands: NAG-NAG.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.522

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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