SMTL ID : 7zyf.2 (1 other biounit)

Insulin regulated aminopeptidase (IRAP) in complex with a nanomolar alpha hydroxy beta amino acid based inhibitor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

monomer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 4 residues within 4Å: Chain A: Y.567, N.604, N.606, Q.651 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.2: 7 residues within 4Å: Chain A: N.30, T.32, S.33, E.131, K.132, D.168, L.189 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.189

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.3: 2 residues within 4Å: Chain A: N.696, K.726 No protein-ligand interaction detected (PLIP)

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.4: 5 residues within 4Å: Chain A: F.642, Q.646, Q.650, G.679, N.680 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.650

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.310, E.311, H.314, E.333 Ligands: KFR.19 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.310, A:H.314, A:E.333, A:E.333

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)(Non-functional Binders)

NAG.6: 3 residues within 4Å: Chain A: Q.45, G.100, N.102 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.45 NAG.7: 2 residues within 4Å: Chain A: N.220, Q.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.220, A:Q.257 NAG.14: 5 residues within 4Å: Chain A: G.508, R.509, N.510, S.512 Ligands: NAG.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.508, A:R.509, A:S.512 NAG.15: 2 residues within 4Å: Chain A: T.530 Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Ligands: NAG.17 No protein-ligand interaction detected (PLIP) NAG.17: 4 residues within 4Å: Chain A: N.214, L.215, S.216 Ligands: NAG.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.216, A:S.216 NAG.18: 6 residues within 4Å: Chain A: G.59, H.60, N.61, S.110, A.111, N.112 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.61 Hydrogen bonds: A:G.59, A:N.61, A:N.112

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

EDO.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.9: 1 residues within 4Å: Chain A: E.350 No protein-ligand interaction detected (PLIP) EDO.10: 1 residues within 4Å: Chain A: Q.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.48 EDO.12: 4 residues within 4Å: Chain A: Q.650, Q.651, Q.652, T.653 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.651

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.11: 2 residues within 4Å: Chain A: D.632, R.636 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.632, A:R.636

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

PEG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x KFR: methyl (2S)-2-[[(2S)-2-[[(2S,3R)-3-azanyl-2-oxidanyl-4-(4-oxidanylphenoxy)butanoyl]amino]-4-methyl-pentanoyl]amino]-3-(1H-indol-3-yl)propanoate(Non-covalent)

KFR.19: 17 residues within 4Å: Chain A: Q.139, E.141, P.142, A.273, G.274, A.275, M.276, E.277, I.307, H.310, E.311, H.314, E.333, F.390, Y.395, Y.807 Ligands: ZN.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.273, A:H.310, A:Y.395, A:Y.395, A:Y.395, A:Y.807 Hydrogen bonds: A:Q.139, A:G.274, A:A.275, A:A.275, A:E.277, A:Y.395, A:Y.395 pi-Stacking: A:F.390, A:Y.807

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vourloumis, D. et al., Discovery of Selective Nanomolar Inhibitors for Insulin-Regulated Aminopeptidase Based on alpha-Hydroxy-beta-amino Acid Derivatives of Bestatin. J.Med.Chem. (2022)

Release Date

2022-07-20

Peptides

Leucyl-cystinyl aminopeptidase, pregnancy serum form: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Leucyl-cystinyl aminopeptidase, pregnancy serum form

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