SMTL ID : 6wyd.2 (3 other biounits)

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-12 (AKA; 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyrid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: L.33 Chain B: R.326, F.327, G.329 Ligands: BMA.2, MAN.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.327 Hydrophobic interactions: A:L.33 NAG.5: 5 residues within 4Å: Chain B: N.77, N.80, A.86, V.87, Q.89 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.86 Hydrogen bonds: B:N.77, B:N.80, B:V.87, B:Q.89, B:Q.89 NAG.6: 5 residues within 4Å: Chain B: N.113, S.115, W.257, L.261 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.113 NAG.7: 1 residues within 4Å: Ligands: NAG.6 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain B: N.205, S.207, V.208 Ligands: FUC.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.205

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

BMA.2: 8 residues within 4Å: Chain B: Y.197, F.327, C.328, C.385, T.389 Ligands: NAG.1, MAN.3, MAN.4 No protein-ligand interaction detected (PLIP)

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

MAN.3: 2 residues within 4Å: Chain B: K.196 Ligands: BMA.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.196, B:K.196 MAN.4: 6 residues within 4Å: Chain A: W.32 Chain B: F.327, K.393 Ligands: NAG.1, BMA.2, FUC.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.393

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

FUC.9: 4 residues within 4Å: Chain B: V.208, R.392 Ligands: MAN.4, NAG.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.208 Hydrogen bonds: B:R.392

1 x HEC: HEME C(Non-covalent)

HEC.10: 24 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: 7GD.11 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:R.221, B:I.227, B:F.253, B:L.294, B:L.294, B:F.295, B:L.305, B:L.305, A:Q.91, A:Q.91, A:D.94 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224 Hydrogen bonds: A:T.100

1 x 7GD: 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine(Non-covalent)

7GD.11: 9 residues within 4Å: Chain A: Q.91, H.95, F.99 Chain B: T.126, R.127, E.130, F.254, F.295 Ligands: HEC.10 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.127, B:E.130, B:F.254, B:F.254, B:F.295 Hydrogen bonds: B:R.127, B:E.130, A:Q.91

1 x CA: CALCIUM ION(Non-covalent)

CA.12: 6 residues within 4Å: Chain A: D.96 Chain B: T.56, S.57, F.58, D.60, S.62 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:T.56, B:F.58, B:S.62, A:D.96, A:D.96

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

CL.13: 3 residues within 4Å: Chain B: N.88, Q.89, F.101 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: R.31, W.32 Chain B: N.214, V.215, W.324 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaw, S.A. et al., Discovery and structure activity relationships of 7-benzyl triazolopyridines as stable, selective, and reversible inhibitors of myeloperoxidase. Bioorg.Med.Chem. (2020)

Release Date

2020-10-14

Peptides

Myeloperoxidase light chain: A
Myeloperoxidase heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

Myeloperoxidase light chain

Myeloperoxidase heavy chain

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