SMTL ID : 8e5m.1 (1 other biounit)

Structure of ARG1 complex with pyrrolidine-based non-boronic acid inhibitor 6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-trimer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.101, D.124, D.128, D.232 Ligands: MN.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.101, A:D.124, A:D.128, A:D.232, H2O.3, H2O.5 MN.2: 5 residues within 4Å: Chain A: D.124, H.126, D.232, D.234 Ligands: MN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.124, A:H.126, A:D.232, A:D.234, H2O.3 MN.4: 5 residues within 4Å: Chain B: H.101, D.124, D.128, D.232 Ligands: MN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.101, B:D.124, B:D.128, B:D.232, H2O.9 MN.5: 5 residues within 4Å: Chain B: D.124, H.126, D.232, D.234 Ligands: MN.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.124, B:H.126, B:D.232, B:D.234, H2O.9 MN.7: 5 residues within 4Å: Chain C: H.101, D.124, D.128, D.232 Ligands: MN.8 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.101, C:D.124, C:D.128, C:D.232, H2O.17 MN.8: 5 residues within 4Å: Chain C: D.124, H.126, D.232, D.234 Ligands: MN.7 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.124, C:H.126, C:D.232, C:D.234, H2O.17

3 x UKR: 1-{[(3S,4S)-3-({4-[2-(4-fluorobenzene-1-sulfonyl)ethyl]piperidin-1-yl}methyl)-4-(3-fluorophenyl)pyrrolidin-1-yl]methyl}cyclopentane-1-carboxylic acid(Non-covalent)

UKR.3: 13 residues within 4Å: Chain A: D.128, N.130, T.136, S.137, H.141, G.142, D.181, D.183, E.186, T.246, P.247, V.248, V.249 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.130, A:S.137 Water bridges: A:S.137, A:S.137, A:N.139, A:N.139, A:H.141 Salt bridges: A:D.181, A:D.181, A:D.183, A:E.186 UKR.6: 13 residues within 4Å: Chain B: H.126, D.128, N.130, T.136, S.137, H.141, G.142, D.181, D.183, E.186, P.247, V.248, V.249 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.126 Hydrogen bonds: B:N.130, B:S.137 Water bridges: B:T.135, B:T.135, B:S.137, B:S.137, B:N.139, B:G.142 Salt bridges: B:D.181, B:D.181, B:D.183 UKR.9: 13 residues within 4Å: Chain C: H.126, D.128, N.130, T.136, S.137, H.141, G.142, D.181, D.183, T.246, P.247, V.248, V.249 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:H.126, C:T.246 Hydrogen bonds: C:N.130, C:S.137 Water bridges: C:T.135, C:T.135, C:S.137, C:S.137, C:N.139, C:H.141 Salt bridges: C:D.181, C:D.181, C:D.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gathiaka, S. et al., Discovery of non-boronic acid Arginase 1 inhibitors through virtual screening and biophysical methods. Bioorg.Med.Chem.Lett. (2023)

Release Date

2023-03-08

Peptides

Arginase-1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

Arginase-1

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