SMTL ID : 6dyy.1 (1 other biounit)

Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-(((3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: T.138, S.139, G.140, S.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.138, A:G.140, A:S.141 EDO.4: 4 residues within 4Å: Chain B: T.138, S.139, G.140, S.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.138, B:G.140, B:S.141, B:S.141 EDO.5: 5 residues within 4Å: Chain A: A.121, F.122 Chain B: G.220, M.221, D.224 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.122, B:G.220 Water bridges: B:D.224 EDO.6: 3 residues within 4Å: Chain B: E.152, Q.153, H.154 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: K.148, E.152, E.244 No protein-ligand interaction detected (PLIP)

2 x OS6: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl]sulfanyl}methyl)pyrrolidin-3-ol(Non-covalent)

OS6.3: 22 residues within 4Å: Chain A: A.24, M.25, I.67, V.93, A.94, G.95, Q.167, F.168, V.169, V.187, E.188, M.189, E.190, S.212, D.213, A.215, F.223 Chain B: L.119, F.122, H.124, P.130, E.131 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.67, B:E.131 Hydrogen bonds: A:V.169, A:E.190, A:D.213, A:D.213 Salt bridges: A:E.28, A:E.190 OS6.8: 21 residues within 4Å: Chain A: L.119, F.122, H.124, P.130 Chain B: A.24, M.25, I.67, V.93, A.94, G.95, Q.167, F.168, V.169, V.187, E.188, M.189, E.190, S.212, D.213, A.215, F.223 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.67, A:F.122, A:P.130 Hydrogen bonds: B:V.169, B:E.190, B:D.213, B:D.213 Salt bridges: B:E.28, B:E.190

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

5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase

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