SMTL ID : 8rgu.1

Arginase 2 in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.115, D.138, D.142, D.246 Ligands: MN.2, DMS.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.115, A:D.138, A:D.142, A:D.246, DMS.3 MN.2: 6 residues within 4Å: Chain A: D.138, H.140, D.246, D.248 Ligands: MN.1, DMS.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.138, A:H.140, A:D.246, A:D.248, DMS.3 MN.6: 6 residues within 4Å: Chain B: H.115, D.138, D.142, D.246 Ligands: MN.7, DMS.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.115, B:D.138, B:D.142, B:D.246, DMS.8 MN.7: 6 residues within 4Å: Chain B: D.138, H.140, D.246, D.248 Ligands: MN.6, DMS.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.138, B:H.140, B:D.246, B:D.248, DMS.8 MN.11: 6 residues within 4Å: Chain C: H.115, D.138, D.142, D.246 Ligands: MN.12, DMS.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.115, C:D.138, C:D.142, C:D.246, DMS.13 MN.12: 6 residues within 4Å: Chain C: D.138, H.140, D.246, D.248 Ligands: MN.11, DMS.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.138, C:H.140, C:D.246, C:D.248, DMS.13

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 11 residues within 4Å: Chain A: H.115, D.138, H.140, D.142, H.155, D.246, D.248, T.260, E.291 Ligands: MN.1, MN.2 6 PLIP interactions: 6 interactions with chain A Salt bridges: A:D.138, A:D.142, A:D.246, A:D.248, A:E.291 pi-Cation interactions: A:H.155 DMS.4: 4 residues within 4Å: Chain A: S.29, Q.32, K.33, N.83 No protein-ligand interaction detected (PLIP) DMS.8: 11 residues within 4Å: Chain B: H.115, D.138, H.140, D.142, H.155, D.246, D.248, T.260, E.291 Ligands: MN.6, MN.7 6 PLIP interactions: 6 interactions with chain B Salt bridges: B:D.138, B:D.142, B:D.246, B:D.248, B:E.291 pi-Cation interactions: B:H.155 DMS.9: 4 residues within 4Å: Chain B: G.221 Chain C: D.218, R.219, G.221 No protein-ligand interaction detected (PLIP) DMS.13: 11 residues within 4Å: Chain C: H.115, D.138, H.140, D.142, H.155, D.246, D.248, T.260, E.291 Ligands: MN.11, MN.12 6 PLIP interactions: 6 interactions with chain C Salt bridges: C:D.138, C:D.142, C:D.246, C:D.248, C:E.291 pi-Cation interactions: C:H.155 DMS.14: 5 residues within 4Å: Chain C: Q.210, Y.211, F.212, D.216, R.228 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.211 Salt bridges: C:D.216

3 x PRO: PROLINE(Non-covalent)

PRO.5: 6 residues within 4Å: Chain A: H.140, N.144, S.151, G.156, D.195, D.197 10 PLIP interactions: 1 Ligand-Ligand interactions, 9 interactions with chain A Water bridges: P.5, A:D.142, A:T.149, A:T.149, A:S.151, A:S.151, A:S.151, A:N.153 Hydrogen bonds: A:N.144, A:S.151 PRO.10: 7 residues within 4Å: Chain B: H.140, N.144, S.151, N.153, G.156, D.195, D.197 10 PLIP interactions: 8 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:H.140 Hydrogen bonds: B:N.144, B:S.151, B:D.197, B:E.200, P.10, P.10 Water bridges: B:T.149, B:N.153, B:N.153 PRO.15: 7 residues within 4Å: Chain C: H.140, N.144, S.151, N.153, G.156, D.195, D.197 10 PLIP interactions: 9 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:H.140 Hydrogen bonds: C:N.144, C:S.151, C:E.200, P.15 Water bridges: C:S.151, C:S.151, C:S.151, C:N.153, C:G.156

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

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