SMTL ID : 7lae.2 (1 other biounit)

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.97 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 5 residues within 4Å: Chain A: L.33 Chain B: R.326, F.327, G.329 Ligands: BMA.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.327 Hydrophobic interactions: A:L.33

1 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.2: 7 residues within 4Å: Chain B: F.327, C.328, C.385, T.389 Ligands: NAG-NAG.1, MAN.3, MAN.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.389

2 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.3: 3 residues within 4Å: Chain B: K.196, C.328 Ligands: BMA.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.196 MAN.4: 5 residues within 4Å: Chain A: W.32 Chain B: F.327, K.393 Ligands: BMA.2, FUC.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.393

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.5: 22 residues within 4Å: Chain A: M.87, G.90, Q.91, D.94, D.98, F.99, T.100 Chain B: R.127, E.130, M.131, T.217, F.220, R.221, G.223, H.224, I.227, L.294, F.295, L.305, L.308, R.312 Ligands: XRV.11 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:R.221, B:I.227, B:L.294, B:L.294, B:F.295, B:L.305, B:L.305, A:Q.91, A:Q.91 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224 Hydrogen bonds: A:T.100

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.6: 6 residues within 4Å: Chain B: N.77, N.80, L.84, A.86, V.87, Q.89 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.86 Hydrogen bonds: B:N.80, B:V.87, B:Q.89, B:Q.89 NAG.7: 5 residues within 4Å: Chain B: N.113, S.115, W.257, L.261 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.113 NAG.8: 1 residues within 4Å: Ligands: NAG.7 No protein-ligand interaction detected (PLIP)

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.9: 4 residues within 4Å: Chain B: V.208, R.392, D.396 Ligands: MAN.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.208

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain A: D.96 Chain B: T.56, F.58, D.60, S.62 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:F.58, B:D.60, B:S.62, A:D.96, A:D.96

1 x XRV: 7-{[1-(4-fluorophenyl)-1H-pyrazol-4-yl]methyl}-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine(Non-covalent)

XRV.11: 11 residues within 4Å: Chain A: Q.91, H.95, F.99 Chain B: L.104, P.108, T.126, R.127, E.130, F.254, F.295 Ligands: HEM.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.254, B:F.295 Hydrogen bonds: B:R.127, B:E.130, A:Q.91 pi-Stacking: B:F.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, C.H. et al., Small molecule and macrocyclic pyrazole derived inhibitors of myeloperoxidase (MPO). Bioorg.Med.Chem.Lett. (2021)

Release Date

2021-04-21

Peptides

Myeloperoxidase light chain: A
Isoform H14 of Myeloperoxidase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

Myeloperoxidase light chain

Isoform H14 of Myeloperoxidase

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