SMTL ID : 9gjn.1 (1 other biounit)

ERAP1 in complex with 1-[2-(3-oxo-3,4-dihydro-2H-1,4-benzothiazin-4-yl)acetamido]cyclohexane-1-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.353, H.357, E.376, Y.438 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.353, A:H.357, A:E.376, A:E.376, H2O.20

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.2: 13 residues within 4Å: Chain A: F.405, D.406, E.409, K.526, N.616, S.623, Q.650, N.653, E.654, P.657, L.661, E.892, W.896 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:F.405, A:D.406, A:E.409, A:K.526, A:N.616, A:S.623, A:Q.650, A:E.654, A:E.892 Water bridges: A:K.526, A:S.623, A:P.657, A:N.893

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

EDO.3: 8 residues within 4Å: Chain A: H.98, E.129, T.185, R.188, M.189, P.426, R.430, E.840 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.129, A:T.185, A:R.188, A:R.430, A:E.840 Water bridges: A:E.840 EDO.4: 7 residues within 4Å: Chain A: T.421, P.422, V.423, Q.428, E.431, M.432, R.881 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.422, A:E.431, A:E.431, A:R.881 Water bridges: A:R.881 EDO.5: 7 residues within 4Å: Chain A: S.340, A.341, S.342, R.700, M.701, S.704, D.741 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.341, A:S.342, A:R.700, A:D.741 Water bridges: A:S.340 EDO.6: 6 residues within 4Å: Chain A: T.643, E.644, I.645, S.698, E.699, L.702 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.644, A:I.645, A:S.698 Water bridges: A:S.696 EDO.7: 8 residues within 4Å: Chain A: L.637, F.677, W.907, L.908, S.910, E.911, K.912, L.913 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.907, A:K.912, A:L.913 EDO.8: 3 residues within 4Å: Chain A: T.559, T.561, D.562 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.562 Water bridges: A:K.560, A:T.561, A:T.561 EDO.9: 4 residues within 4Å: Chain A: D.666, M.667, N.668, E.669 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.668 EDO.10: 3 residues within 4Å: Chain A: V.712, Q.752, R.782 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.712, A:Q.752, A:R.782, A:R.782

5 x BR: BROMIDE ION(Non-covalent)

BR.11: 1 residues within 4Å: Chain A: R.208 Ligand excluded by PLIP BR.12: 3 residues within 4Å: Chain A: T.690, W.691, R.721 Ligand excluded by PLIP BR.13: 2 residues within 4Å: Chain A: R.829, K.830 Ligand excluded by PLIP BR.14: 2 residues within 4Å: Chain A: R.515, N.516 Ligand excluded by PLIP BR.15: 3 residues within 4Å: Chain A: Y.451, T.543, R.554 Ligand excluded by PLIP

1 x 01: 1-[2-(3-oxidanylidene-1,4-benzothiazin-4-yl)ethanoylamino]cyclohexane-1-carboxylic acid

01.16: 12 residues within 4Å: Chain A: N.653, I.656, P.657, Y.659, K.660, Q.705, L.708, H.713, F.778, R.782, R.816, Q.856 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.656, A:L.708, A:F.778 Hydrogen bonds: A:K.660, A:Q.856 Water bridges: A:R.782, A:R.782, A:R.782, A:R.782 Salt bridges: A:K.660, A:H.713, A:R.782

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hryczanek, R.P. et al., Optimization of Potent and Selective Cyclohexyl Acid ERAP1 Inhibitors Using Structure- and Property-Based Drug Design. Acs Med.Chem.Lett. (2024)

Release Date

2025-01-22

Peptides

Endoplasmic reticulum aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endoplasmic reticulum aminopeptidase 1

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