SMTL ID : 7lag.4 (3 other biounits)

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-14 AKA 7-({1-[(3-phenoxyphenyl)methyl]-1H-pyrazol-4-yl}methyl)-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.1: 12 residues within 4Å: Chain A: W.32, L.33 Chain B: K.196, Y.197, R.326, F.327, C.328, G.329, C.385, K.393 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.2, NAG-NAG-BMA-MAN-MAN-FUC.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.393 Hydrophobic interactions: A:L.33 NAG-NAG-BMA-MAN-MAN-FUC.2: 6 residues within 4Å: Chain B: N.205, S.207, V.208, R.392 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.1, NAG-NAG-BMA-MAN-MAN-FUC.1 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.208

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

HEM.3: 24 residues within 4Å: Chain A: M.87, G.90, Q.91, D.94, D.98, F.99, T.100, E.102 Chain B: R.127, E.130, M.131, T.217, F.220, R.221, G.223, H.224, I.227, F.253, L.294, F.295, L.305, L.308, R.312 Ligands: XSD.7 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain B, Hydrophobic interactions: A:Q.91, A:Q.91, B:F.220, B:F.220, B:R.221, B:I.227, B:F.253, B:L.294, B:L.294, B:F.295, B:L.305, B:L.305 Hydrogen bonds: A:D.98, A:T.100, A:T.100 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224

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

NAG.4: 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 Hydrogen bonds: B:N.77, B:N.80, B:V.87, B:Q.89, B:Q.89 NAG.5: 4 residues within 4Å: Chain B: N.113, S.115, W.257, L.261 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.113

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.96 Chain B: T.56, F.58, D.60, S.62 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:D.96, A:D.96, B:T.56, B:F.58, B:S.62

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

XSD.7: 10 residues within 4Å: Chain A: Q.91, H.95, F.99 Chain B: P.108, T.126, R.127, E.130, F.254, F.295 Ligands: HEM.3 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.108, B:R.127, B:F.254, B:F.295 Hydrogen bonds: B:R.127, A:Q.91, A:H.95

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
H

B
I

Myeloperoxidase light chain

Isoform H14 of Myeloperoxidase

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