SMTL ID : 4ixv.3 (3 other biounits)

Crystal structure of human Arginase-2 complexed with inhibitor 2d: {(5R)-5-amino-5-carboxy-5-[1-(4-chlorobenzyl)piperidin-4-yl]pentyl}(trihydroxy)borate(1-)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.97, D.120, D.124, D.228 Ligands: MN.2, XA1.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.97, A:D.120, A:D.124, A:D.228 MN.2: 6 residues within 4Å: Chain A: D.120, H.122, D.228, D.230 Ligands: MN.1, XA1.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.120, A:H.122, A:D.228, A:D.230, A:D.230

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.3: 3 residues within 4Å: Chain A: N.60, N.61, L.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.60

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 6 residues within 4Å: Chain A: H.1, V.3, L.38, G.39, C.40, F.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.300

1 x XA1: {(5R)-5-amino-5-carboxy-5-[1-(4-chlorobenzyl)piperidin-4-yl]pentyl}(trihydroxy)borate(1-)(Non-covalent)

XA1.5: 16 residues within 4Å: Chain A: H.97, D.120, H.122, D.124, N.126, S.132, S.133, H.137, G.138, D.179, D.228, D.230, T.242, E.273 Ligands: MN.1, MN.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.126, A:S.133, A:D.179, A:T.242, A:E.273 Water bridges: A:D.124, A:S.133, A:S.133, A:N.135, A:G.138, A:G.138, A:D.179, A:E.273 Salt bridges: A:D.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Golebiowski, A. et al., Synthesis of quaternary alpha-amino acid-based arginase inhibitors via the Ugi reaction. Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-12-11

Peptides

Arginase-2, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Arginase-2, mitochondrial

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