SMTL ID : 6en5.4 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: N.45, T.47, E.49, N.50, R.53, R.326 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.49

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.2: 5 residues within 4Å: Chain A: N.416, E.522, G.523, P.524, Q.527 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.522 Hydrophobic interactions: A:P.524

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, N.480, T.482, H.483, L.603 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.478, A:T.478, 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: 24 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, R.381, 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 28 PLIP interactions: 28 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.332, A:A.334, A:Y.369, A:Y.369, A:Y.369, A:H.491, A:Y.498, A:Y.498, A:Y.501 Water bridges: A:R.381, A:R.381, A:R.381, 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.5, H2O.20, H2O.20

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

PEG.8: 7 residues within 4Å: Chain A: V.36, S.39, S.333, A.334, W.335, F.490 Ligands: BJ2.5 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain A: R.96, D.189, G.190, F.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:T.97

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

EDO.10: 6 residues within 4Å: Chain A: E.305, L.306, S.307, P.308, Q.371, R.541 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.371, A:R.541 EDO.11: 4 residues within 4Å: Chain A: W.201, R.381, P.385, R.500 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.381, A:S.548 EDO.12: 4 residues within 4Å: Chain A: R.235, R.236, Y.237, G.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.235, A:Y.237

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

ACT.13: 5 residues within 4Å: Chain A: R.199, E.208, W.447, S.451, R.453 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.447 Water bridges: A:R.199, A:G.448 Salt bridges: A:R.199 ACT.14: 5 residues within 4Å: Chain A: N.606, E.609, G.610, D.612, L.613 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.613

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

XPE.15: 10 residues within 4Å: Chain A: Q.286, G.287, W.288, T.291, H.292, R.295, V.296, E.299, I.408, Y.531 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.292 Water bridges: A:E.299

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

2017-12-20

Peptides

Angiotensin-converting enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Angiotensin-converting enzyme

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