SMTL ID : 6dz0.1

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-((pent-4-yn-1-ylthio)methyl)pyrrolidin-3-ol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-trimer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: OS3.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.32, A:A.108, A:T.211 Salt bridges: A:R.74, A:H.75 PO4.9: 8 residues within 4Å: Chain B: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: OS3.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.32, B:A.108, 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: OS3.23 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.32, C:A.108, C:T.211 Salt bridges: C:R.74, C:H.75

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

EDO.2: 6 residues within 4Å: Chain A: D.129, R.130, T.131, Q.136 Chain B: R.130, T.132 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Water bridges: B:R.130, B:T.132, A:T.131 Hydrogen bonds: A:R.130, A:T.131, A:T.131, A:Q.136 EDO.3: 3 residues within 4Å: Chain A: E.115, Q.117, R.176 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.115, A:Q.117, A:R.176, A:R.176 EDO.4: 5 residues within 4Å: Chain A: A.23, V.24, N.66, V.67, D.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.24, A:D.68, A:D.68 EDO.5: 4 residues within 4Å: Chain A: Y.235, K.239, E.242, E.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.239, A:E.243, A:E.243 EDO.6: 4 residues within 4Å: Chain A: L.175, R.176, C.177, H.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.175, A:C.177, A:H.178 EDO.10: 6 residues within 4Å: Chain B: D.129, R.130, T.131, Q.136 Chain C: R.130, T.132 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.130, B:T.131, B:T.131, B:Q.136 Water bridges: B:T.131, C:R.130, C:T.132 EDO.11: 3 residues within 4Å: Chain B: E.115, Q.117, R.176 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.115, B:Q.117, B:R.176, B:R.176 EDO.12: 5 residues within 4Å: Chain B: A.23, V.24, N.66, V.67, D.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.24, B:D.68, B:D.68 EDO.13: 4 residues within 4Å: Chain B: Y.235, K.239, E.242, E.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.239, B:E.243, B:E.243 EDO.14: 4 residues within 4Å: Chain B: L.175, R.176, C.177, H.178 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.175, B:C.177, B:H.178 EDO.18: 6 residues within 4Å: Chain A: R.130, T.132 Chain C: D.129, R.130, T.131, Q.136 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.130, C:T.131, C:T.131, C:Q.136 Water bridges: C:T.131, A:R.130, A:T.132 EDO.19: 3 residues within 4Å: Chain C: E.115, Q.117, R.176 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.115, C:Q.117, C:R.176, C:R.176 EDO.20: 5 residues within 4Å: Chain C: A.23, V.24, N.66, V.67, D.68 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.24, C:D.68, C:D.68 EDO.21: 4 residues within 4Å: Chain C: Y.235, K.239, E.242, E.243 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.239, C:E.243, C:E.243 EDO.22: 4 residues within 4Å: Chain C: L.175, R.176, C.177, H.178 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.175, C:C.177, C:H.178

3 x OS3: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol(Non-covalent)

OS3.7: 23 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 Chain C: V.149, H.151, S.291, L.293 Ligands: PO4.1 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:V.149, C:L.293, C:L.293, A:T.32 Hydrogen bonds: A:T.32, A:D.234, A:D.236, A:D.236 pi-Stacking: A:F.191 OS3.15: 23 residues within 4Å: Chain A: V.149, H.151, S.291, 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 Ligands: PO4.9 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.32, A:V.149, A:L.293, A:L.293 Hydrogen bonds: B:T.32, B:D.234, B:D.236, B:D.236 pi-Stacking: B:F.191 OS3.23: 23 residues within 4Å: Chain B: V.149, H.151, S.291, 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 Ligands: PO4.17 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:V.149, B:L.293, B:L.293, C:T.32 Hydrogen bonds: C:T.32, C:D.234, C:D.236, C:D.236 pi-Stacking: C:F.191

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

CL.8: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.16, CL.24 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.8, CL.24 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.8, CL.16 Ligand excluded by PLIP

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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