SMTL ID : 7ni3.2 (1 other biounit)

CRYSTAL STRUCTURE OF NATIVE HUMAN MYELOPEROXIDASE IN COMPLEX WITH CPD 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- FUC: 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-FUC.1: 7 residues within 4Å: Chain B: R.202, N.205, S.207, V.208, R.392, K.393 Ligands: BMA.6 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.208, B:K.393

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: R.31, W.32 Chain B: N.214, V.215, W.324 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: Q.91, H.95 Chain B: R.127, E.130 Ligands: HEM.3, UE8.5 Ligand excluded by PLIP

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.3: 25 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, Y.184, 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: CL.4, UE8.5 25 PLIP interactions: 18 interactions with chain B, 6 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:E.130, B:M.131, B:F.220, B:R.221, B:I.227, B:F.253, B:L.294, B:F.295, B:L.305, B:L.305, A:Q.91, A:Q.91 Water bridges: B:R.221, B:R.221, B:R.221, B:R.312 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224, H2O.2 Hydrogen bonds: A:D.98, A:D.98, A:T.100, A:T.100

1 x UE8: 2-sulfanylidene-3-[(2R)-tetrahydro-2-furanylmethyl]-1,2,3,7-tetrahydro-6H-purin-6-one(Non-covalent)

UE8.5: 8 residues within 4Å: Chain A: F.99, T.100, E.102 Chain B: R.127, E.130, F.295 Ligands: HEM.3, CL.4 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.127, A:E.102 Water bridges: A:Q.91, A:H.95

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

BMA.6: 3 residues within 4Å: Chain B: F.327, K.393 Ligands: NAG-NAG-BMA-FUC.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.393 Water bridges: B:K.393

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 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.80, B:V.87, B:Q.89, B:Q.89 Water bridges: B:N.77 NAG.8: 6 residues within 4Å: Chain B: N.113, S.115, A.116, R.251, W.257, L.261 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.251 Water bridges: B:R.258

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain A: D.96 Chain B: T.56, F.58, D.60, S.62 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Metal complexes: A:D.96, B:T.56, B:F.58, B:D.60, B:S.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inghardt, T. et al., Discovery of AZD4831, a Mechanism-Based Irreversible Inhibitor of Myeloperoxidase, As a Potential Treatment for Heart Failure with Preserved Ejection Fraction. J.Med.Chem. (2022)

Release Date

2022-02-23

Peptides

Myeloperoxidase: A
Myeloperoxidase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Myeloperoxidase

Myeloperoxidase

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