SMTL ID : 6en6.4 (3 other biounits)

Crystal structure B of the Angiotensin-1 converting enzyme N-domain in complex with a diprolyl inhibitor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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.1: 7 residues within 4Å: Chain A: N.45, T.47, E.49, N.50, R.53, D.324, R.326 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.49

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 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.3: 8 residues within 4Å: Chain A: V.477, T.478, R.479, N.480, T.482, H.483, L.603 Ligands: ACT.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.482, A:T.478 Water bridges: A:R.479

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: H.361, H.365, E.389, Y.501 Ligands: BJ2.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.361, A:H.365, A:E.389

1 x BJ2: (2~{S})-1-[(2~{S})-2-[[(1~{S})-1-[(2~{S})-1-[(2~{S})-2-azanyl-4-oxidanyl-4-oxidanylidene-butanoyl]pyrrolidin-2-yl]-2-oxidanyl-2-oxidanylidene-ethyl]amino]propanoyl]pyrrolidine-2-carboxylic acid(Non-covalent)

BJ2.5: 23 residues within 4Å: Chain A: Q.259, H.331, A.332, S.333, A.334, T.358, H.361, E.362, H.365, Y.369, E.389, F.435, K.489, F.490, H.491, T.496, Y.498, R.500, Y.501, F.505 Ligands: ZN.4, PEG.8, EDO.16 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.490, A:T.496, A:Y.501 Hydrogen bonds: A:Q.259, A:H.331, A:A.334, A:E.362, A:Y.369, A:Y.369, A:H.491, A:Y.498, A:Y.501 Water bridges: A:R.381, A:R.381, A:R.381, A:E.389, A:K.489, A:K.489, A:R.500 Salt bridges: A:H.331, A:H.361, A:H.365, A:H.365, A:H.388, A:K.489, A:H.491

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

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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: S.260, E.262, N.263, D.354 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.262, A:D.354, H2O.4, H2O.19, H2O.20

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

PEG.8: 6 residues within 4Å: Chain A: V.36, S.39, S.333, A.334, W.335 Ligands: BJ2.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.39, A:S.39 PEG.9: 3 residues within 4Å: Chain A: H.406, K.407, G.409 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.406

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

EDO.10: 6 residues within 4Å: Chain A: F.33, A.37, W.40, F.337, D.342, R.344 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.342, A:R.344, A:R.344 Water bridges: A:A.37, A:A.37 EDO.11: 2 residues within 4Å: Chain A: P.311, E.315 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.312, A:E.315 EDO.12: 2 residues within 4Å: Chain A: T.302, P.308 No protein-ligand interaction detected (PLIP) EDO.13: 2 residues within 4Å: Chain A: R.541, R.545 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.541 EDO.14: 4 residues within 4Å: Chain A: R.96, D.189, G.190, F.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.189 EDO.15: 6 residues within 4Å: Chain A: W.40, T.44, G.316, S.317, M.318, R.326 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.317, A:R.326 Water bridges: A:R.326 EDO.16: 8 residues within 4Å: Chain A: W.201, R.381, P.385, T.496, P.497, R.500 Ligands: BJ2.5, EDO.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.500, A:R.500 Water bridges: A:R.381 EDO.17: 4 residues within 4Å: Chain A: W.201, R.381, P.385 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.381, A:R.381 Water bridges: A:G.382 EDO.18: 3 residues within 4Å: Chain A: D.209, E.212, Q.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.216

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.19: 5 residues within 4Å: Chain A: E.609, G.610, D.612, L.613 Ligands: ACT.22 No protein-ligand interaction detected (PLIP) ACT.20: 5 residues within 4Å: Chain A: R.199, E.208, W.447, G.448, S.451 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.199, A:Q.444 Salt bridges: A:R.199 ACT.21: 5 residues within 4Å: Chain A: E.513, D.566, Q.568, P.569, K.572 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.568 Salt bridges: A:K.572 ACT.22: 5 residues within 4Å: Chain A: N.606, E.609, G.610, L.613 Ligands: ACT.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.606 ACT.23: 6 residues within 4Å: Chain A: V.477, T.478, P.601, P.602, L.603 Ligands: NAG-FUC.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.478

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

PGE.24: 7 residues within 4Å: Chain A: Q.444, W.445, G.448, T.454, D.462, Y.465, L.466 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.444 Water bridges: A:V.449, A:T.454, A:T.454 PGE.25: 6 residues within 4Å: Chain A: W.464, Y.465, T.468, Y.597, Q.598, H.600 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.464 PGE.26: 8 residues within 4Å: Chain A: Q.289, E.320, K.321, P.322, A.323, G.325, T.349, R.350 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.322 Water bridges: A:K.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fienberg, S. et al., The Design and Development of a Potent and Selective Novel Diprolyl Derivative That Binds to the N-Domain of Angiotensin-I Converting Enzyme. J. Med. Chem. (2018)

Release Date

2018-03-07

Peptides

Angiotensin-converting enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Angiotensin-converting enzyme

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