SMTL ID : 6en6.1 (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: 6 residues within 4Å: Chain A: N.45, T.47, E.49, N.50, D.324, R.326 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: 9 residues within 4Å: Chain A: E.403, N.416, D.417, T.418, D.421, E.522, G.523, P.524, Q.527 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.522, A:E.522, A:E.522, A:N.416, A:T.418 Water bridges: A:D.421

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

NAG-NAG-FUC.3: 5 residues within 4Å: Chain A: T.478, R.479, N.480, T.482, H.483 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.480

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, H.388, 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 24 PLIP interactions: 24 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:E.389, A:K.489, A:K.489, A:R.500, 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.2, H2O.15, H2O.19

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

PEG.8: 8 residues within 4Å: Chain A: S.333, A.334, W.335, F.490, N.494, T.496 Ligands: BJ2.5, EDO.11 No protein-ligand interaction detected (PLIP) PEG.9: 6 residues within 4Å: Chain A: L.32, Y.338, V.377, S.378, R.380, R.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.377 Water bridges: A:R.381

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

EDO.10: 5 residues within 4Å: Chain A: R.295, E.298, P.308, M.309, W.314 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.295, A:E.298, A:W.314 Water bridges: A:M.309, A:M.309 EDO.11: 7 residues within 4Å: Chain A: L.115, S.119, P.493, N.494, V.495, T.496 Ligands: PEG.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.494 Water bridges: A:L.115

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

ACT.12: 4 residues within 4Å: Chain A: R.199, E.208, W.447, S.451 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.447 Water bridges: A:R.199, A:W.447, A:G.448 Salt bridges: A:R.199 ACT.13: 4 residues within 4Å: Chain A: E.513, Q.568, P.569, K.572 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.568

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

PGE.14: 10 residues within 4Å: Chain A: H.42, I.46, T.47, A.48, A.51, S.116, Q.117, R.120, T.124, E.327 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.42, A:I.46, A:S.116 Water bridges: A:R.120

1 x BCN: BICINE(Non-covalent)

BCN.15: 2 residues within 4Å: Chain A: R.453, Y.465 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.453, A:R.453

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
A

Angiotensin-converting enzyme

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