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

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH COMPOUND-18 AKA 7-(3-(2,3-DIHYDRO-1H-INDEN-1-YLAMINO)-1-PHENYLPROPYL)-1H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN-5-AMINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-mer

Ligands

2 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: 10 residues within 4Å: Chain A: L.33 Chain B: Y.197, R.326, F.327, C.328, G.329, C.385, T.389 Ligands: MAN.3, MAN.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.389, B:T.389 Hydrophobic interactions: A:L.33 NAG-NAG-BMA-FUC.2: 6 residues within 4Å: Chain B: N.205, S.207, V.208, R.392, D.396 Ligands: MAN.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.208 Hydrogen bonds: B:R.392

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

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

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 23 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, R.312 Ligands: XSG.10 20 PLIP interactions: 6 interactions with chain A, 14 interactions with chain B, Hydrophobic interactions: A:Q.91, A:Q.91, A:D.94, B:M.131, B:F.220, B:F.220, B:R.221, B:I.227, B:F.253, 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

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

NAG.6: 6 residues within 4Å: Chain B: N.77, N.80, L.84, A.86, V.87, Q.89 7 PLIP interactions: 7 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, B:Q.89 NAG.7: 4 residues within 4Å: Chain B: N.113, W.257, L.261 Ligands: NAG.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.113, B:L.261 NAG.8: 1 residues within 4Å: Ligands: NAG.7 No protein-ligand interaction detected (PLIP)

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: 5 interactions with chain B Metal complexes: B:T.56, B:T.56, B:F.58, B:D.60, B:S.62

1 x XSG: 7-[(1R)-3-{[(1R)-2,3-dihydro-1H-inden-1-yl]amino}-1-phenylpropyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine(Non-covalent)

XSG.10: 12 residues within 4Å: Chain A: Q.91, H.95, F.99, E.102 Chain B: P.108, T.126, R.127, E.130, F.254, V.298, M.299 Ligands: HEM.5 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.108, B:P.108, B:R.127, B:E.130, B:F.254, B:F.254, B:V.298 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
D

B
E

Myeloperoxidase light chain

Isoform H14 of Myeloperoxidase

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