SMTL ID : 6dz2.1

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-(((3-(1-benzyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-trimer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: L.294 Ligands: EDO.8 No protein-ligand interaction detected (PLIP) EDO.2: 1 residues within 4Å: Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.3: 3 residues within 4Å: Chain A: K.255 Ligands: EDO.2, EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.255 EDO.8: 5 residues within 4Å: Chain A: F.290, V.292, L.293 Chain B: D.248 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.290 EDO.11: 3 residues within 4Å: Chain C: T.275, E.276 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain C: S.274 Ligands: EDO.11, EDO.14, EDO.16 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain C: L.293, L.294 Ligands: EDO.3, EDO.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.294 EDO.14: 2 residues within 4Å: Ligands: EDO.12, EDO.16 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: D.248 Chain C: F.290, V.292 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.248 EDO.16: 2 residues within 4Å: Ligands: EDO.12, EDO.14 No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: T.107, N.209, M.210, T.211 Ligands: OS5.7 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: T.107, N.209, M.210, T.211 Ligands: OS5.10 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain C: T.107, N.209, M.210, T.211 Ligands: OS5.18 Ligand excluded by PLIP

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.6: 6 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 No protein-ligand interaction detected (PLIP)

3 x OS5: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[3-(1-benzyl-1H-1,2,3-triazol-4-yl)propyl]sulfanyl}methyl)pyrrolidin-3-ol(Non-covalent)

OS5.7: 24 residues within 4Å: Chain A: G.30, T.32, P.83, T.106, T.107, 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.250, L.254, A.258, A.261 Chain C: H.151, L.293 Ligands: CL.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.32, A:T.106, A:L.254, A:A.258, A:A.261 Hydrogen bonds: A:T.233, A:D.234, A:D.236, A:D.236 Water bridges: A:A.108, A:A.108 pi-Stacking: A:F.191 OS5.10: 23 residues within 4Å: Chain A: H.151, L.293 Chain B: G.30, T.32, P.83, T.106, T.107, 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.250, L.254, A.258 Ligands: CL.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.32, B:L.254, B:L.254, B:A.258 Hydrogen bonds: B:A.108, B:T.233, B:D.234, B:D.236, B:D.236 pi-Stacking: B:F.191 OS5.18: 22 residues within 4Å: Chain B: H.151, L.293 Chain C: T.32, P.83, T.107, 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.250, L.251, L.254, A.258 Ligands: CL.17 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:T.32, C:V.250, C:L.251, C:L.254, C:A.258 Hydrogen bonds: C:T.233, C:D.234, C:D.236, C:D.236 Water bridges: C:A.108, C:A.108 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
B

C
C

S-methyl-5'-thioadenosine phosphorylase

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