SMTL ID : 5qj2.3 (3 other biounits)

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) OMPLEX WITH COMPOUND-20 AKA 7-((3-(1-METHYL-1H-PYRAZOL-3- YL)BENZYL)OXY)- 1H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN-5-AMINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain B: N.78, N.81, L.85, A.87, V.88, Q.90 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.87 Hydrogen bonds: B:N.78, B:N.81, B:V.88, B:Q.90, B:Q.90 NAG.2: 5 residues within 4Å: Chain B: N.114, S.116, W.258, L.262 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.114 NAG.3: 1 residues within 4Å: Ligands: NAG.2 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain B: N.206, S.208, V.209 Ligands: FUC.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.206 NAG.6: 4 residues within 4Å: Chain B: T.434, F.450, V.451, N.452 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.434 Hydrogen bonds: B:N.452 NAG.8: 6 residues within 4Å: Chain A: L.33 Chain B: R.327, F.328, G.330 Ligands: BMA.9, MAN.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.33

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

FUC.5: 4 residues within 4Å: Chain B: V.209, R.393 Ligands: NAG.4, MAN.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.209

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

HEM.7: 24 residues within 4Å: Chain A: M.87, G.90, Q.91, D.94, D.98, F.99, T.100 Chain B: R.128, E.131, M.132, Y.185, T.218, F.221, R.222, Y.223, G.224, H.225, I.228, L.295, F.296, L.306, L.309, R.313 Ligands: JXS.12 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A, Hydrophobic interactions: B:M.132, B:F.221, B:F.221, B:R.222, B:Y.223, B:I.228, B:L.295, B:L.295, B:F.296, B:L.306, B:L.306, A:Q.91, A:Q.91 Salt bridges: B:R.128, B:R.222, B:R.313 Metal complexes: B:H.225 Hydrogen bonds: A:D.98, A:T.100, A:T.100

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

BMA.9: 8 residues within 4Å: Chain B: Y.198, F.328, C.329, G.330, T.390 Ligands: NAG.8, MAN.10, MAN.11 No protein-ligand interaction detected (PLIP)

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

MAN.10: 4 residues within 4Å: Chain B: K.197, C.329, G.330 Ligands: BMA.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.197, B:G.330 MAN.11: 6 residues within 4Å: Chain A: W.32 Chain B: F.328, K.394 Ligands: FUC.5, NAG.8, BMA.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.394

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

JXS.12: 9 residues within 4Å: Chain A: Q.91, H.95, F.99 Chain B: T.127, R.128, E.131, F.255, F.296 Ligands: HEM.7 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.128, B:F.255 Hydrogen bonds: B:T.127, B:R.128, B:E.131, A:Q.91 pi-Stacking: A:F.99

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 5 residues within 4Å: Chain A: D.96 Chain B: T.57, F.59, D.61, S.63 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:T.57, B:F.59, B:S.63, A:D.96, A:D.96

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

CL.14: 2 residues within 4Å: Chain B: N.89, F.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wurtz, N.R. et al., Potent Triazolopyridine Myeloperoxidase Inhibitors. ACS Med Chem Lett (2018)

Release Date

2019-02-06

Peptides

Myeloperoxidase: A
Myeloperoxidase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

Myeloperoxidase

Myeloperoxidase

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