SMTL ID : 6en5.2 (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: 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: 5 residues within 4Å: Chain A: 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- 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: 4 residues within 4Å: Chain A: T.478, N.480, T.482, H.483 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.480 Water bridges: A:T.478, A:T.478

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, EDO.13 25 PLIP interactions: 25 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:A.334, A:Y.369, A:Y.369, A:H.491, A:Y.498, A:Y.498, A:Y.501 Water bridges: 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.3, H2O.16, H2O.18

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

PEG.8: 6 residues within 4Å: Chain A: W.80, R.96, T.97, D.189, G.190, F.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 PEG.9: 6 residues within 4Å: Chain A: F.271, T.418, E.419, I.422, W.580, Q.584 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.419, A:E.419, A:W.580, A:Q.584 Water bridges: A:T.418 PEG.10: 8 residues within 4Å: Chain A: F.33, A.37, W.40, A.41, F.337, N.339, D.342, R.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.342, A:R.344, A:R.344 PEG.11: 3 residues within 4Å: Chain A: R.235 Ligands: PEG.12, PG4.20 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.235 PEG.12: 4 residues within 4Å: Chain A: R.235, R.236 Ligands: PEG.11, PG4.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.235, A:R.235

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

EDO.13: 4 residues within 4Å: Chain A: S.333, A.334, W.335 Ligands: BJ2.5 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain A: E.518, T.534, K.535, A.538 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.534 EDO.15: 6 residues within 4Å: Chain A: Y.24, L.32, Y.338, V.377, S.378, R.381 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.338 EDO.16: 3 residues within 4Å: Chain A: R.120, I.121, P.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.120 Water bridges: A:A.166 EDO.17: 4 residues within 4Å: Chain A: R.231, H.234, L.244, N.588 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.231, A:R.231

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

ACT.18: 4 residues within 4Å: Chain A: R.199, E.208, W.447, S.451 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.447 Hydrogen bonds: A:W.447 Water bridges: A:R.199, A:R.199, A:R.199, A:R.453 Salt bridges: A:R.199

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

PGE.19: 4 residues within 4Å: Chain A: T.454, D.462, Y.465, L.466 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.448

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

PG4.20: 12 residues within 4Å: Chain A: F.228, R.231, A.232, R.235, M.267, V.268, V.269, P.270, P.272, N.588 Ligands: PEG.11, PEG.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.235, A:R.235 Water bridges: A:N.588, A:N.588

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
B

Angiotensin-converting enzyme

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