SMTL ID : 7jr6.1

H-PDGS complexed with a 2-phenylimidazo[1,2-a]pyridine-6-carboxamide inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 15 residues within 4Å: Chain A: Y.9, F.10, R.15, W.40, K.44, G.50, K.51, I.52, P.53, Q.64, S.65, L.66 Chain B: D.94, D.98 Ligands: VH4.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:K.51 Hydrogen bonds: A:R.15, A:W.40, A:I.52, A:I.52, A:Q.64, A:Q.64, A:S.65, A:S.65 Water bridges: A:R.15, A:R.15, A:Q.64, A:Q.64, A:L.66, A:D.97, A:D.97 Salt bridges: A:R.15, A:K.44 GSH.6: 16 residues within 4Å: Chain A: D.94, D.98 Chain B: Y.9, F.10, M.12, R.15, W.40, K.44, G.50, K.51, I.52, P.53, Q.64, S.65, L.66 Ligands: VH4.7 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.15, B:W.40, B:K.51, B:I.52, B:I.52, B:Q.64, B:S.65, B:S.65, A:D.98 Water bridges: B:R.15, B:R.15, B:R.15, B:Q.64, B:L.66, A:D.94, A:D.94 Salt bridges: B:R.15, B:K.51

2 x VH4: 1-(3-fluorophenyl)-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide(Non-covalent)

VH4.2: 15 residues within 4Å: Chain A: Y.9, F.10, M.12, G.14, R.15, Q.37, D.97, M.100, S.101, W.105, A.106, Y.153, T.160, L.200 Ligands: GSH.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.15, A:W.105, A:W.105, A:A.106 Hydrogen bonds: A:Q.37, A:T.160 Water bridges: A:L.200 pi-Stacking: A:W.105 Halogen bonds: A:S.101 VH4.7: 16 residues within 4Å: Chain B: Y.9, F.10, M.12, G.14, R.15, Q.37, W.40, D.97, M.100, S.101, W.105, A.106, Y.153, T.160, L.200 Ligands: GSH.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.15, B:Q.37, B:W.105 pi-Stacking: B:W.105 Halogen bonds: B:S.101

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: D.97 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: E.83 Chain B: Y.71 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: D.77, G.80, N.81, S.146, V.147, T.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.81, A:V.147 Water bridges: A:S.146 NA.5: 4 residues within 4Å: Chain A: K.165, D.167, D.170, N.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.167 Water bridges: A:K.165, A:N.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulte, C.A. et al., A knowledge-based, structural-aided discovery of a novel class of 2-phenylimidazo[1,2-a]pyridine-6-carboxamide H-PGDS inhibitors. Bioorg.Med.Chem.Lett. (2021)

Release Date

2021-05-26

Peptides

Hematopoietic prostaglandin D synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hematopoietic prostaglandin D synthase

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