SMTL ID : 6en6.2 (3 other biounits)

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

Coordinates

PDB Format

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, D.324, R.326 Ligands: EDO.17 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.3: 6 residues within 4Å: Chain A: V.477, T.478, N.480, T.482, H.483, L.603 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.482 Water bridges: A:H.483, A:T.478, A:T.478, A:N.480 Hydrophobic interactions: 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, PEG.9 23 PLIP interactions: 23 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:A.334, A:E.362, A:Y.369, A:H.491, A:Y.498, A:R.500, A:Y.501 Water bridges: A:E.389, A:K.489, A:K.489 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.7, H2O.18

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

PEG.8: 8 residues within 4Å: Chain A: Y.24, A.28, L.32, F.64, Y.338, V.377, S.378, R.381 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.338 PEG.9: 6 residues within 4Å: Chain A: V.36, S.39, S.333, A.334, W.335 Ligands: BJ2.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.39, A:S.39 Water bridges: A:S.35 PEG.10: 6 residues within 4Å: Chain A: F.33, A.37, W.40, F.337, D.342, R.344 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.40, A:D.342, A:R.344, A:R.344 PEG.11: 5 residues within 4Å: Chain A: W.80, R.96, D.189, G.190, F.191 No protein-ligand interaction detected (PLIP)

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

EDO.12: 4 residues within 4Å: Chain A: L.221, L.571, Q.575, T.578 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.217, A:L.571, A:F.574 EDO.13: 12 residues within 4Å: Chain A: W.160, H.164, M.256, W.257, F.438, W.463, W.464, R.467, D.485, A.486, A.488, K.489 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.257, A:W.463, A:R.467, A:R.467, A:D.485 EDO.14: 1 residues within 4Å: Chain A: Y.465 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain A: E.212, H.213, Q.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.213, A:Q.216 EDO.16: 8 residues within 4Å: Chain A: S.204, T.206, D.210, W.552, Q.553, D.563, A.564, L.565 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.553, A:D.563 EDO.17: 4 residues within 4Å: Chain A: A.41, N.50, R.53 Ligands: NAG-NAG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.50, A:N.50, A:R.53 Water bridges: A:N.45 EDO.18: 5 residues within 4Å: Chain A: I.46, T.47, R.120, T.124, E.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.120 Water bridges: A:I.46 EDO.19: 2 residues within 4Å: Chain A: Q.285, Q.286 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.285, A:Q.286

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

ACT.20: 5 residues within 4Å: Chain A: R.199, E.208, W.447, G.448, S.451 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.199, A:W.447, A:G.448 Salt bridges: A:R.199 ACT.21: 4 residues within 4Å: Chain A: E.55, A.113, S.116, Q.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.117 Water bridges: A:R.52 ACT.22: 5 residues within 4Å: Chain A: E.513, D.566, Q.568, P.569, K.572 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.568

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

PGE.23: 9 residues within 4Å: Chain A: T.192, A.196, R.199, S.200, S.204, P.205, T.206, F.207, E.208 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.199, A:R.199, A:E.208 Water bridges: A:S.204, A:P.205, A:D.209 PGE.24: 5 residues within 4Å: Chain A: R.231, H.234, D.239, L.244, R.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.239, A:R.245 Water bridges: A:L.244, A:R.245

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.25: 11 residues within 4Å: Chain A: F.228, R.231, A.232, R.235, R.236, M.267, V.268, V.269, P.270, P.272, N.588 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.235, A:R.235, A:R.235

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

XPE.26: 9 residues within 4Å: Chain A: Q.286, G.287, W.288, T.291, H.292, R.295, V.296, E.299, I.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.292

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
B

Angiotensin-converting enzyme

Related Entries With Identical Sequence