SMTL ID : 6dyz.1

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((prop-2-yn-1-ylthio)methyl)pyrrolidin-3-ol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: CL.8, CL.15 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.9, CL.16 Ligand excluded by PLIP CL.8: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: CL.1, CL.15 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.2, CL.16 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: CL.1, CL.8 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.2, CL.9 Ligand excluded by PLIP

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: OS2.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.32, A:A.108, A:T.211 Water bridges: A:T.211 Salt bridges: A:R.74, A:H.75 PO4.10: 8 residues within 4Å: Chain B: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: OS2.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.32, B:A.108, B:T.211 Water bridges: B:T.211 Salt bridges: B:R.74, B:H.75 PO4.17: 8 residues within 4Å: Chain C: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: OS2.21 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.32, C:A.108, C:T.211 Water bridges: C:T.211 Salt bridges: C:R.74, C:H.75

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

EDO.4: 7 residues within 4Å: Chain A: D.129, R.130, T.131 Chain B: R.130, T.132 Ligands: EDO.11, EDO.18 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.130, A:R.130 EDO.5: 3 residues within 4Å: Chain A: L.175, R.176, C.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.175, A:C.177 EDO.6: 3 residues within 4Å: Chain A: E.115, K.180, D.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.115, A:E.115, A:K.180 EDO.11: 7 residues within 4Å: Chain B: D.129, R.130, T.131 Chain C: R.130, T.132 Ligands: EDO.4, EDO.18 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.130, C:R.130 EDO.12: 3 residues within 4Å: Chain B: L.175, R.176, C.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.175, B:C.177 EDO.13: 3 residues within 4Å: Chain B: E.115, K.180, D.206 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.115, B:E.115, B:K.180 EDO.18: 7 residues within 4Å: Chain A: R.130, T.132 Chain C: D.129, R.130, T.131 Ligands: EDO.4, EDO.11 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.130, C:R.130 EDO.19: 3 residues within 4Å: Chain C: L.175, R.176, C.177 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.175, C:C.177 EDO.20: 3 residues within 4Å: Chain C: E.115, K.180, D.206 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.115, C:E.115, C:K.180

3 x OS2: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(prop-2-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol(Non-covalent)

OS2.7: 22 residues within 4Å: Chain A: T.32, H.75, H.79, P.83, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.245, V.247, V.250, L.251 Chain C: H.151, L.293 Ligands: PO4.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.247, C:L.293 Hydrogen bonds: A:T.32, A:D.234, A:D.236, A:D.236 pi-Stacking: A:F.191 OS2.14: 22 residues within 4Å: Chain A: H.151, L.293 Chain B: T.32, H.75, H.79, P.83, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.245, V.247, V.250, L.251 Ligands: PO4.10 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.247, A:L.293 Hydrogen bonds: B:T.32, B:D.234, B:D.236, B:D.236 pi-Stacking: B:F.191 OS2.21: 22 residues within 4Å: Chain B: H.151, L.293 Chain C: T.32, H.75, H.79, P.83, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.245, V.247, V.250, L.251 Ligands: PO4.17 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.247, B:L.293 Hydrogen bonds: C:T.32, C:D.234, C:D.236, C:D.236 pi-Stacking: C:F.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harijan, R.K. et al., Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase. J. Med. Chem. (2019)

Release Date

2019-03-20

Peptides

S-methyl-5'-thioadenosine phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

S-methyl-5'-thioadenosine phosphorylase

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