SMTL ID : 7klk.1 (1 other biounit)

Human Arginase1 Complexed with Inhibitor Compound 3a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.101, D.124, D.128, D.232 Ligands: MN.2, XFP.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.101, A:D.124, A:D.128, A:D.232, XFP.3 MN.2: 7 residues within 4Å: Chain A: D.124, H.126, D.232, D.234, T.246 Ligands: MN.1, XFP.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.124, A:H.126, A:D.232, A:D.234, XFP.3 MN.4: 6 residues within 4Å: Chain B: H.101, D.124, D.128, D.232 Ligands: MN.5, XFP.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.101, B:D.124, B:D.128, B:D.232 MN.5: 6 residues within 4Å: Chain B: D.124, H.126, D.232, D.234 Ligands: MN.4, XFP.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.124, B:H.126, B:D.232, B:D.234, XFP.6 MN.7: 6 residues within 4Å: Chain C: H.101, D.124, D.128, D.232 Ligands: MN.8, XFP.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.101, C:D.124, C:D.128, C:D.232 MN.8: 6 residues within 4Å: Chain C: D.124, H.126, D.232, D.234 Ligands: MN.7, XFP.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.124, C:H.126, C:D.232, C:D.234, XFP.9

3 x XFP: 3-[(2~{S},3~{R})-2-carboxypiperidin-3-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide(Non-covalent)

XFP.3: 18 residues within 4Å: Chain A: H.101, D.124, H.126, D.128, N.130, S.137, N.139, H.141, G.142, D.181, D.183, E.186, D.232, D.234, T.246, E.277 Ligands: MN.1, MN.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.130, A:S.137, A:N.139, A:H.141, A:T.246 Water bridges: A:S.137, A:S.137, A:S.137, A:N.139, A:N.139, A:E.186, A:T.246, A:E.277 XFP.6: 17 residues within 4Å: Chain B: H.101, D.124, H.126, D.128, N.130, S.137, H.141, G.142, D.181, D.183, E.186, D.232, D.234, T.246, E.277 Ligands: MN.4, MN.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.130, B:S.137, B:H.141 Water bridges: B:H.101, B:T.135, B:S.137, B:S.137, B:S.137, B:N.139, B:N.139, B:E.186, B:T.246 XFP.9: 17 residues within 4Å: Chain C: H.101, D.124, H.126, D.128, N.130, S.137, H.141, G.142, D.181, D.183, E.186, D.232, D.234, T.246, E.277 Ligands: MN.7, MN.8 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.130, C:S.137, C:N.139, C:H.141, C:E.186, C:T.246, C:T.246 Water bridges: C:T.135, C:T.135, C:S.137, C:N.139, C:T.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, M. et al., Structure-Based Discovery of Proline-Derived Arginase Inhibitors with Improved Oral Bioavailability for Immuno-Oncology. Acs Med.Chem.Lett. (2021)

Release Date

2021-09-29

Peptides

Arginase-1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

Arginase-1

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