SMTL ID : 5wdj.1

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH COMPOUND-6 AKA 7-(BENZYLOXY)-1H-[1,2, 3]TRIAZOLO[4,5-D]PYRIMIDIN-5-AMINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-BMA-MAN.1: 9 residues within 4Å: Chain B: S.208 Chain C: L.33 Chain D: K.197, Y.198, R.327, F.328, G.330 Ligands: NAG.7, MAN.17 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:K.197, D:K.197 Hydrophobic interactions: C:L.33 Water bridges: B:S.208

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 11 residues within 4Å: Chain A: L.33 Chain B: Y.198, R.327, F.328, G.330 Chain D: N.206, S.208, V.209 Ligands: MAN.11, MAN.12, FUC.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.33

2 x AEY: 7-(benzyloxy)-1H-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine(Non-covalent)

AEY.3: 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.5 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.128, B:F.255, B:F.255, A:F.99 Hydrogen bonds: B:R.128, B:E.131, A:Q.91 Water bridges: B:R.222 AEY.21: 9 residues within 4Å: Chain C: Q.91, H.95, F.99 Chain D: T.127, R.128, E.131, F.255, F.296 Ligands: HEM.14 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:R.128, D:F.255, D:F.255 Hydrogen bonds: D:R.128, D:E.131, C:Q.91 Water bridges: C:T.100

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

CL.4: 5 residues within 4Å: Chain A: R.31, W.32 Chain B: N.215, V.216, W.325 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: N.89, Q.90, F.102 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain C: V.30, R.31, W.32 Chain D: N.215, V.216, W.325 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain D: N.89, Q.90, F.102 Ligand excluded by PLIP

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 22 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, T.218, F.221, R.222, G.224, H.225, I.228, F.254, L.295, F.296, L.306, R.313 Ligands: AEY.3 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:E.131, B:M.132, B:F.221, B:R.222, B:I.228, B:F.254, 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:T.100 HEM.14: 22 residues within 4Å: Chain C: M.87, G.90, Q.91, D.94, D.98, F.99, T.100 Chain D: R.128, E.131, M.132, Y.185, T.218, F.221, R.222, G.224, H.225, I.228, F.254, F.296, L.306, R.313 Ligands: AEY.21 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain C, Hydrophobic interactions: D:E.131, D:M.132, D:R.222, D:I.228, D:F.254, D:F.296, D:L.306, D:L.306, C:Q.91, C:Q.91 Water bridges: D:T.218, D:R.222 Salt bridges: D:R.128, D:R.222, D:R.313 Metal complexes: D:H.225 Hydrogen bonds: C:D.98, C:T.100, C:T.100

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.96 Chain B: T.57, F.59, D.61, S.63 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:T.57, B:F.59, B:D.61, B:S.63, A:D.96 CA.16: 5 residues within 4Å: Chain C: D.96 Chain D: T.57, F.59, D.61, S.63 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Metal complexes: D:T.57, D:F.59, D:D.61, D:S.63, C:D.96

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

NAG.7: 5 residues within 4Å: Chain B: N.206, V.209 Chain D: R.327 Ligands: NAG-BMA-MAN.1, FUC.8 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.327 Water bridges: B:N.206 NAG.9: 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.10: 5 residues within 4Å: Chain B: N.114, S.116, A.117, W.258, L.262 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.114, B:N.114 NAG.19: 6 residues within 4Å: Chain D: N.78, N.81, L.85, A.87, V.88, Q.90 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.87 Hydrogen bonds: D:N.81, D:V.88, D:Q.90, D:Q.90 Water bridges: D:N.78, D:N.78 NAG.20: 5 residues within 4Å: Chain D: N.114, S.116, A.117, W.258, L.262 No protein-ligand interaction detected (PLIP)

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

FUC.8: 4 residues within 4Å: Chain B: V.209, R.393 Ligands: NAG.7, MAN.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.209, B:R.393 Water bridges: B:K.394 FUC.18: 4 residues within 4Å: Chain D: R.393 Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2, MAN.17 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:R.393 Water bridges: D:R.393

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

MAN.11: 2 residues within 4Å: Chain B: K.197 Ligands: NAG-NAG-BMA.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.197 MAN.12: 5 residues within 4Å: Chain A: W.32 Chain B: F.328, K.394 Ligands: NAG-NAG-BMA.2, FUC.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.394, A:W.32 Water bridges: B:K.394 MAN.17: 5 residues within 4Å: Chain C: W.32 Chain D: F.328, K.394 Ligands: NAG-BMA-MAN.1, FUC.18 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.394 Water bridges: D:K.394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duclos, F. et al., Triazolopyrimidines identified as reversible myeloperoxidase inhibitors. Medchemcomm (2017)

Release Date

2018-04-18

Peptides

Myeloperoxidase: AC
Myeloperoxidase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

Myeloperoxidase

Myeloperoxidase

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