Chlorine in PDB 6dz2: 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

Enzymatic activity of 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

All present enzymatic activity of 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:
2.4.2.28;

Protein crystallography data

The structure of 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, PDB code: 6dz2 was solved by R.K.Harijan, R.G.Ducati, J.B.Bonanno, S.C.Almo, V.L.Schramm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.63 / 1.99
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.390, 135.316, 159.268, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 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 (pdb code 6dz2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the 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, PDB code: 6dz2:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6dz2

Go back to Chlorine Binding Sites List in 6dz2
Chlorine binding site 1 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:24.4
occ:1.00
 O A:HOH494 2.7 33.2 1.0
NH1 A:ARG116 3.2 24.6 1.0
NH1 B:ARG116 3.2 25.8 1.0
NH1 C:ARG116 3.3 23.9 1.0
CD A:ARG116 3.8 21.3 1.0
CD C:ARG116 3.8 23.1 1.0
CD B:ARG116 3.9 23.3 1.0
O A:HOH475 4.2 45.4 1.0
CZ A:ARG116 4.2 23.0 1.0
CH2 B:TRP189 4.2 26.5 1.0
CH2 C:TRP189 4.3 27.5 1.0
CZ C:ARG116 4.3 23.0 1.0
CZ B:ARG116 4.3 24.2 1.0
O A:HOH465 4.4 46.9 1.0
CH2 A:TRP189 4.5 27.6 1.0
NE A:ARG116 4.5 21.5 1.0
NE C:ARG116 4.5 21.6 1.0
NE B:ARG116 4.6 22.2 1.0
CZ3 B:TRP189 4.9 27.9 1.0
CZ3 C:TRP189 5.0 27.1 1.0

Chlorine binding site 2 out of 4 in 6dz2

Go back to Chlorine Binding Sites List in 6dz2
Chlorine binding site 2 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:35.8
occ:1.00
 OG1 A:THR197 3.0 31.0 1.0
N A:MET196 3.1 23.6 1.0
CG2 A:THR197 3.5 28.8 1.0
N A:THR197 3.5 27.4 1.0
OG1 A:THR93 3.5 32.5 1.0
CB A:ASN195 3.6 22.8 1.0
O A:HOH473 3.6 34.6 1.0
N A:OS5307 3.7 29.0 1.0
CB A:THR197 3.7 30.3 1.0
CA A:MET196 3.8 25.1 1.0
C14 A:OS5307 3.8 30.4 1.0
C7 A:OS5307 3.8 28.5 1.0
C A:MET196 3.9 25.9 1.0
CB A:MET196 3.9 26.6 1.0
ND2 A:ASN195 4.0 23.9 1.0
CG A:ASN195 4.0 21.8 1.0
O A:OS5307 4.1 39.1 1.0
C A:ASN195 4.2 21.7 1.0
O A:ALA94 4.2 28.6 1.0
CA A:THR197 4.2 29.2 1.0
CA A:ASN195 4.3 21.5 1.0
C15 A:OS5307 4.6 34.9 1.0
OD1 A:ASN195 4.8 22.2 1.0
CB A:THR93 4.8 30.3 1.0
CG A:MET196 4.8 27.0 1.0
O A:MET196 4.9 27.1 1.0

Chlorine binding site 3 out of 4 in 6dz2

Go back to Chlorine Binding Sites List in 6dz2
Chlorine binding site 3 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:37.5
occ:1.00
 OG1 B:THR197 3.1 35.1 1.0
N B:MET196 3.1 25.5 1.0
O B:HOH418 3.4 43.3 1.0
N B:THR197 3.5 27.2 1.0
N B:OS5303 3.5 36.0 1.0
CG2 B:THR197 3.5 34.6 1.0
OG1 B:THR93 3.6 37.7 1.0
CB B:ASN195 3.6 25.3 1.0
C7 B:OS5303 3.7 31.8 1.0
CA B:MET196 3.8 26.6 1.0
CB B:THR197 3.8 32.6 1.0
C14 B:OS5303 3.9 36.0 1.0
C B:MET196 3.9 26.9 1.0
CB B:MET196 3.9 25.9 1.0
ND2 B:ASN195 4.0 27.0 1.0
CG B:ASN195 4.0 25.9 1.0
O B:OS5303 4.1 41.7 1.0
C B:ASN195 4.1 24.4 1.0
CA B:ASN195 4.2 23.6 1.0
O B:ALA94 4.2 31.7 1.0
CA B:THR197 4.3 29.4 1.0
C15 B:OS5303 4.7 39.5 1.0
CG B:MET196 4.7 25.6 1.0
C6 B:OS5303 4.7 37.2 1.0
OD1 B:ASN195 4.8 28.3 1.0
O B:MET196 4.9 27.8 1.0
CB B:THR93 4.9 34.9 1.0

Chlorine binding site 4 out of 4 in 6dz2

Go back to Chlorine Binding Sites List in 6dz2
Chlorine binding site 4 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl307

b:35.5
occ:1.00
 N C:MET196 3.2 25.0 1.0
OG1 C:THR197 3.2 31.6 1.0
C7 C:OS5308 3.4 27.6 1.0
N C:OS5308 3.5 29.3 1.0
O C:HOH457 3.5 54.5 1.0
C14 C:OS5308 3.6 33.0 1.0
CG2 C:THR197 3.6 32.1 1.0
CB C:ASN195 3.6 26.0 1.0
N C:THR197 3.6 28.1 1.0
OG1 C:THR93 3.7 34.7 1.0
CA C:MET196 3.8 25.7 1.0
CB C:THR197 3.9 31.4 1.0
CB C:MET196 4.0 27.7 1.0
C C:MET196 4.0 27.1 1.0
CG C:ASN195 4.1 27.2 1.0
ND2 C:ASN195 4.1 27.6 1.0
O C:ALA94 4.1 29.9 1.0
C C:ASN195 4.2 24.9 1.0
CA C:ASN195 4.2 24.6 1.0
CA C:THR197 4.4 29.5 1.0
O C:OS5308 4.5 37.0 1.0
C15 C:OS5308 4.7 35.8 1.0
CG C:MET196 4.7 28.0 1.0
C8 C:OS5308 4.8 26.0 1.0
OD1 C:ASN195 4.9 25.7 1.0
C6 C:OS5308 4.9 32.6 1.0
CB C:THR93 5.0 35.2 1.0
O C:MET196 5.0 28.6 1.0
N4 C:OS5308 5.0 24.1 1.0

Reference:

R.K.Harijan, O.Hoff, R.G.Ducati, R.S.Firestone, B.M.Hirsch, G.B.Evans, V.L.Schramm, P.C.Tyler. Selective Inhibitors of Helicobacter Pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase. J. Med. Chem. V. 62 3286 2019.
ISSN: ISSN 1520-4804
PubMed: 30860833
DOI: 10.1021/ACS.JMEDCHEM.8B01642
Page generated: Sat Dec 12 12:54:18 2020

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