SMTL ID : 6q39.1

Complex of Arginase 2 with Example 49

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-trimer

Ligands

6 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, HDQ.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, HDQ.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 MN.6: 6 residues within 4Å: Chain B: H.97, D.120, D.124, D.228 Ligands: MN.7, HDQ.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.97, B:D.120, B:D.124, B:D.228 MN.7: 6 residues within 4Å: Chain B: D.120, H.122, D.228, D.230 Ligands: MN.6, HDQ.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.120, B:H.122, B:D.228, B:D.230, B:D.230 MN.11: 6 residues within 4Å: Chain C: D.120, H.122, D.228, D.230 Ligands: MN.12, HDQ.15 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.120, C:H.122, C:D.228, C:D.230, C:D.230 MN.12: 6 residues within 4Å: Chain C: H.97, D.120, D.124, D.228 Ligands: MN.11, HDQ.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.97, C:D.120, C:D.124, C:D.228

3 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 BEN.8: 3 residues within 4Å: Chain B: N.60, N.61, L.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.60 BEN.13: 3 residues within 4Å: Chain C: N.60, N.61, L.62 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.60

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

BME.4: 6 residues within 4Å: Chain A: V.3, L.38, G.39, C.40, H.261, F.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.300 BME.9: 6 residues within 4Å: Chain B: H.1, V.3, L.38, G.39, C.40, F.300 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.300 BME.14: 6 residues within 4Å: Chain C: H.1, V.3, L.38, G.39, C.40, F.300 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.300

3 x HDQ: 3-[(3~{S},4~{R})-4-azanyl-4-carboxy-1-[[(2~{S})-piperidin-2-yl]methyl]pyrrolidin-3-yl]propyl-tris(oxidanyl)boranuide(Non-covalent)

HDQ.5: 17 residues within 4Å: Chain A: H.97, D.120, H.122, D.124, N.126, S.133, H.137, G.138, D.177, D.179, E.182, D.228, D.230, T.242, E.273 Ligands: MN.1, MN.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.126, A:S.133, A:H.137, A:D.177, A:D.179 Water bridges: A:D.124, A:T.131, A:T.131, A:S.133, A:S.133, A:G.138, A:D.179, A:T.242, A:T.242 Salt bridges: A:D.177, A:D.179 HDQ.10: 17 residues within 4Å: Chain B: H.97, D.120, H.122, D.124, N.126, S.133, H.137, G.138, D.177, D.179, E.182, D.228, D.230, T.242, E.273 Ligands: MN.6, MN.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.126, B:S.133, B:H.137, B:D.179, B:T.242, B:E.273 Water bridges: B:D.124, B:S.133, B:S.133, B:S.133, B:G.138, B:G.138, B:D.179, B:E.273 Salt bridges: B:D.177, B:D.179 HDQ.15: 17 residues within 4Å: Chain C: H.97, D.120, H.122, D.124, N.126, S.133, H.137, G.138, D.177, D.179, E.182, D.228, D.230, T.242, E.273 Ligands: MN.11, MN.12 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:H.122 Hydrogen bonds: C:N.126, C:S.133, C:D.179, C:E.273 Water bridges: C:D.124, C:T.131, C:T.131, C:S.133, C:S.133, C:S.133, C:N.135, C:D.179, C:D.179, C:T.242 Salt bridges: C:D.177, C:D.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Zandt, M.C. et al., Discovery ofN-Substituted 3-Amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic Acids as Highly Potent Third-Generation Inhibitors of Human Arginase I and II. J.Med.Chem. (2019)

Release Date

2019-08-28

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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