SMTL ID : 7jr8.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: A.187, N.190, R.194 Ligand excluded by PLIP

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: K.51 Chain B: F.99, N.124, H.127, L.128, D.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.51 EDO.3: 7 residues within 4Å: Chain A: E.85, H.88, Y.135, R.139, L.142, I.143, G.144 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.135, A:G.144 Water bridges: A:R.139, A:G.144 EDO.6: 7 residues within 4Å: Chain B: E.85, H.88, Y.135, R.139, L.142, I.143, G.144 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.135, B:R.139, B:G.144 Water bridges: B:E.85, B:E.85

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.4: 16 residues within 4Å: Chain A: 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 Chain B: D.94, D.98 Ligands: VH7.5 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.51 Hydrogen bonds: A:I.52, A:I.52, A:Q.64, A:Q.64, A:S.65, A:S.65, B:D.98 Water bridges: A:R.15, A:W.40, A:K.44, A:G.50, A:L.66 Salt bridges: A:R.15 GSH.7: 15 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 Ligands: VH7.8 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:K.51 Hydrogen bonds: B:R.15, B:W.40, B:I.52, B:I.52, B:Q.64, B:Q.64, B:S.65, B:S.65 Water bridges: B:R.15, B:R.15, B:R.15, B:K.44, B:K.51, B:K.51, B:K.51, B:K.51, B:Q.64, B:Q.64, B:D.97 Salt bridges: B:K.44, B:K.51

2 x VH7: N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-2-phenylimidazo[1,2-a]pyridine-6-carboxamide(Non-covalent)

VH7.5: 16 residues within 4Å: Chain A: F.10, M.12, G.14, R.15, Q.37, W.40, D.97, M.100, W.105, A.106, Y.153, I.156, C.157, T.160, L.200 Ligands: GSH.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.10, A:F.10, A:R.15, A:W.40, A:M.100, A:W.105, A:A.106, A:L.200 Water bridges: A:G.14, A:K.113 pi-Stacking: A:W.105, A:W.105, A:W.105 VH7.8: 17 residues within 4Å: Chain B: F.10, M.12, G.14, R.15, Q.37, W.40, D.97, M.100, S.101, W.105, A.106, Y.153, I.156, C.157, T.160, L.200 Ligands: GSH.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.10, B:F.10, B:R.15, B:M.100, B:W.105, B:A.106, B:L.200, B:L.200 Water bridges: B:R.15, B:K.113, B:L.200 pi-Stacking: B:W.105, B:W.105, B:W.105

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain A: D.98 Chain B: D.97 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain B: D.77, A.79, N.81, S.146, T.148 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.77, B:A.79, H2O.14, H2O.16, H2O.20

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

NA.11: 2 residues within 4Å: Chain B: K.180, Q.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.183 Water bridges: B:Q.183 NA.12: 4 residues within 4Å: Chain A: D.98, S.101 Chain B: D.98, S.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.98, A:D.98 NA.13: 1 residues within 4Å: Chain B: Y.135 No protein-ligand interaction detected (PLIP)

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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