SMTL ID : 7zyf.1 (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

1 x NAG- NAG- BMA- MAN: 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.1: 9 residues within 4Å: Chain A: H.28, P.29, N.30, T.32, E.131, K.132, D.168, L.189 Ligands: PEG.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.130, A:K.132, A:K.132, A:T.32, A:T.32 Hydrophobic interactions: A:T.32

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.214, S.216, L.223 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: V.219, N.220, Q.251, E.255, Q.257 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.510, S.512, T.530, E.531 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.530

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: 3 residues within 4Å: Chain A: N.696, K.726, S.729 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: H.310, H.314, E.333 Ligands: KFR.11 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.310, A:H.314, A:E.333

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 5 residues within 4Å: Chain A: R.22, Q.45, G.100, H.101, N.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.22, A:G.100 NAG.8: 2 residues within 4Å: Chain A: Q.650, N.680 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.680 NAG.9: 4 residues within 4Å: Chain A: G.59, H.60, N.61, N.112 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain A: N.371, K.460, N.484 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.460

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.11: 18 residues within 4Å: Chain A: Q.139, E.141, P.142, E.272, 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.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.139, A:A.273, A:I.307, A:I.307, A:F.390, A:Y.807, A:Y.807, A:Y.807 Hydrogen bonds: A:E.272, A:G.274, A:A.275, A:A.275, A:E.333, A:Y.395

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

EDO.12: 2 residues within 4Å: Chain A: E.128, S.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.129 EDO.13: 1 residues within 4Å: Chain A: D.789 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.789 EDO.14: 2 residues within 4Å: Chain A: R.509, L.534 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.509

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

PEG.15: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP) PEG.16: 1 residues within 4Å: Chain A: K.865 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.865

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
A

Leucyl-cystinyl aminopeptidase, pregnancy serum form

Related Entries With Identical Sequence