SMTL ID : 8rgf.1

Arginase 2 in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-trimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.114, D.137, D.141, D.245 Ligands: MN.2, 01.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.114, A:D.137, A:D.141, A:D.245 MN.2: 6 residues within 4Å: Chain A: D.137, H.139, D.245, D.247 Ligands: MN.1, 01.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.137, A:H.139, A:D.245, A:D.247, A:D.247 MN.4: 5 residues within 4Å: Chain B: H.114, D.137, D.141, D.245 Ligands: MN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.114, B:D.137, B:D.141, B:D.245, H2O.6 MN.5: 5 residues within 4Å: Chain B: D.137, H.139, D.245, D.247 Ligands: MN.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.137, B:H.139, B:D.245, B:D.247, H2O.6 MN.6: 6 residues within 4Å: Chain C: H.114, D.137, D.141, D.245 Ligands: MN.7, 01.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.114, C:D.137, C:D.141, C:D.245 MN.7: 6 residues within 4Å: Chain C: D.137, H.139, D.245, D.247 Ligands: MN.6, 01.8 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.137, C:H.139, C:D.245, C:D.247, C:D.247

2 x 01: 4-[(2~{R},4~{R})-4-azanyl-2-carboxy-pyrrolidin-2-yl]butyl-tris(oxidanyl)boranuide

01.3: 17 residues within 4Å: Chain A: H.114, D.137, H.139, D.141, N.143, S.150, H.154, G.155, D.194, D.196, E.199, D.245, D.247, T.259, E.290 Ligands: MN.1, MN.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.143, A:S.150, A:G.155, A:D.194, A:D.196, A:D.247 Water bridges: A:D.141, A:S.150, A:G.155, A:G.155, A:E.290 01.8: 17 residues within 4Å: Chain C: H.114, D.137, H.139, D.141, N.143, S.150, H.154, G.155, D.194, D.196, E.199, D.245, D.247, T.259, E.290 Ligands: MN.6, MN.7 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:T.259 Hydrogen bonds: C:N.143, C:S.150, C:H.154, C:D.196, C:D.196, C:T.259, C:E.290 Water bridges: C:D.141, C:T.148, C:T.148, C:S.150, C:S.150, C:G.155, C:T.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mlynarski, S.N. et al., Discovery of (2 R ,4 R )-4-(( S )-2-Amino-3-methylbutanamido)-2-(4-boronobutyl)pyrrolidine-2-carboxylic Acid (AZD0011), an Actively Transported Prodrug of a Potent Arginase Inhibitor to Treat Cancer. J.Med.Chem. (2024)

Release Date

2024-12-04

Peptides

Arginase-2, mitochondrial: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Arginase-2, mitochondrial