Atomistry » Chlorine » PDB 6dy1-6e74 » 6dz3
Atomistry »
  Chlorine »
    PDB 6dy1-6e74 »
      6dz3 »

Chlorine in PDB 6dz3: 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-Butyl-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-Butyl-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-Butyl-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-Butyl-1H-1,2,3-Triazol-4-Yl) Propyl)Thio)Methyl)Pyrrolidin-3-Ol, PDB code: 6dz3 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) 79.43 / 1.91
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.355, 135.133, 158.860, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22

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-Butyl-1H-1,2,3-Triazol-4-Yl) Propyl)Thio)Methyl)Pyrrolidin-3-Ol (pdb code 6dz3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 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-Butyl-1H-1,2,3-Triazol-4-Yl) Propyl)Thio)Methyl)Pyrrolidin-3-Ol, PDB code: 6dz3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6dz3

Go back to Chlorine Binding Sites List in 6dz3
Chlorine binding site 1 out of 5 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-Butyl-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-Butyl-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:Cl301

b:21.6
occ:1.00
O A:HOH526 2.9 33.4 1.0
NH1 A:ARG116 3.2 20.9 1.0
NH1 B:ARG116 3.3 21.7 1.0
NH1 C:ARG116 3.3 21.2 1.0
CD A:ARG116 3.8 19.9 1.0
CD C:ARG116 3.8 21.0 1.0
CD B:ARG116 3.9 19.7 1.0
CH2 B:TRP189 4.2 23.1 1.0
CZ A:ARG116 4.2 20.9 1.0
CH2 C:TRP189 4.2 22.3 1.0
O A:HOH471 4.3 33.4 1.0
CZ C:ARG116 4.3 21.5 1.0
CZ B:ARG116 4.3 20.5 1.0
O B:HOH482 4.4 38.8 1.0
CH2 A:TRP189 4.4 22.7 1.0
NE A:ARG116 4.5 20.2 1.0
NE C:ARG116 4.5 21.1 1.0
NE B:ARG116 4.6 19.2 1.0
O C:HOH448 4.7 40.8 1.0
CZ3 B:TRP189 4.8 22.6 1.0
CZ3 C:TRP189 4.9 22.6 1.0

Chlorine binding site 2 out of 5 in 6dz3

Go back to Chlorine Binding Sites List in 6dz3
Chlorine binding site 2 out of 5 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-Butyl-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-Butyl-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:Cl302

b:30.6
occ:1.00
OG1 A:THR197 3.0 24.4 1.0
N A:MET196 3.1 20.9 1.0
CG2 A:THR197 3.4 25.3 1.0
N A:THR197 3.5 22.8 1.0
OG1 A:THR93 3.5 29.2 1.0
O A:HOH497 3.5 27.9 1.0
CB A:ASN195 3.6 20.2 1.0
N A:OS6306 3.6 26.8 1.0
C7 A:OS6306 3.7 25.2 1.0
CB A:THR197 3.7 24.6 1.0
C14 A:OS6306 3.7 28.4 1.0
CA A:MET196 3.8 22.4 1.0
C A:MET196 3.9 22.0 1.0
CB A:MET196 4.0 23.2 1.0
ND2 A:ASN195 4.0 20.8 1.0
CG A:ASN195 4.0 20.3 1.0
C A:ASN195 4.2 20.5 1.0
CA A:THR197 4.2 23.5 1.0
O A:ALA94 4.2 22.8 1.0
CA A:ASN195 4.3 20.0 1.0
O A:OS6306 4.4 35.4 1.0
C15 A:OS6306 4.8 31.1 1.0
CG A:MET196 4.8 23.4 1.0
CB A:THR93 4.8 27.6 1.0
OD1 A:ASN195 4.8 20.4 1.0
O A:MET196 4.9 23.7 1.0
C8 A:OS6306 5.0 23.2 1.0
C6 A:OS6306 5.0 28.8 1.0

Chlorine binding site 3 out of 5 in 6dz3

Go back to Chlorine Binding Sites List in 6dz3
Chlorine binding site 3 out of 5 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-Butyl-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-Butyl-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:Cl301

b:31.0
occ:1.00
N B:MET196 3.1 23.4 1.0
OG1 B:THR197 3.1 27.0 1.0
O B:HOH437 3.4 32.7 1.0
N B:OS6303 3.5 30.8 1.0
OG1 B:THR93 3.5 33.8 1.0
C7 B:OS6303 3.5 27.2 1.0
N B:THR197 3.6 23.1 1.0
CG2 B:THR197 3.6 28.0 1.0
CB B:ASN195 3.6 23.2 1.0
C14 B:OS6303 3.7 31.2 1.0
CA B:MET196 3.8 23.4 1.0
CB B:THR197 3.9 27.7 1.0
CB B:MET196 4.0 23.9 1.0
C B:MET196 4.0 23.4 1.0
CG B:ASN195 4.0 22.3 1.0
ND2 B:ASN195 4.0 22.7 1.0
C B:ASN195 4.1 22.4 1.0
O B:OS6303 4.1 34.9 1.0
O B:ALA94 4.2 27.0 1.0
CA B:ASN195 4.2 22.2 1.0
CA B:THR197 4.3 25.1 1.0
C15 B:OS6303 4.6 33.4 1.0
CG B:MET196 4.7 23.6 1.0
C6 B:OS6303 4.8 30.8 1.0
OD1 B:ASN195 4.8 22.9 1.0
CB B:THR93 4.8 31.7 1.0
C8 B:OS6303 4.9 25.8 1.0
O B:MET196 5.0 23.6 1.0

Chlorine binding site 4 out of 5 in 6dz3

Go back to Chlorine Binding Sites List in 6dz3
Chlorine binding site 4 out of 5 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-Butyl-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-Butyl-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:Cl301

b:31.2
occ:1.00
O C:HOH473 3.0 36.0 1.0
N C:GLU100 3.2 24.6 1.0
NH1 C:ARG187 3.3 26.7 1.0
CA C:ARG99 3.8 23.6 1.0
CB C:GLU100 3.9 27.0 1.0
NH2 C:ARG187 4.0 28.8 1.0
C C:ARG99 4.0 24.4 1.0
CZ C:ARG187 4.1 27.5 1.0
CH2 C:TRP224 4.1 26.3 1.0
CA C:GLU100 4.2 25.6 1.0
CD C:ARG99 4.4 24.7 1.0
CB C:ARG99 4.4 23.9 1.0
CZ3 C:TRP224 4.6 28.6 1.0
O C:LEU98 4.7 21.7 1.0
CZ2 C:TRP224 4.8 28.2 1.0
NH1 C:ARG99 4.8 26.6 1.0
N C:ARG99 5.0 22.9 1.0

Chlorine binding site 5 out of 5 in 6dz3

Go back to Chlorine Binding Sites List in 6dz3
Chlorine binding site 5 out of 5 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-Butyl-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 5 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-Butyl-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:Cl302

b:32.0
occ:1.00
N C:MET196 3.2 22.4 1.0
OG1 C:THR197 3.2 28.8 1.0
O C:HOH480 3.3 44.9 1.0
C7 C:OS6307 3.5 23.9 1.0
CG2 C:THR197 3.5 27.6 1.0
N C:OS6307 3.6 25.5 1.0
N C:THR197 3.6 23.4 1.0
C14 C:OS6307 3.6 27.2 1.0
CB C:ASN195 3.6 21.8 1.0
OG1 C:THR93 3.6 25.2 1.0
CA C:MET196 3.8 22.6 1.0
CB C:THR197 3.8 26.7 1.0
CB C:MET196 3.9 24.6 1.0
C C:MET196 4.0 23.5 1.0
CG C:ASN195 4.0 21.9 1.0
ND2 C:ASN195 4.1 22.4 1.0
C C:ASN195 4.2 21.7 1.0
O C:ALA94 4.2 25.2 1.0
CA C:ASN195 4.2 20.9 1.0
CA C:THR197 4.3 24.8 1.0
O C:OS6307 4.6 32.7 1.0
CG C:MET196 4.7 24.1 1.0
C8 C:OS6307 4.8 22.8 1.0
C15 C:OS6307 4.8 30.6 1.0
OD1 C:ASN195 4.8 22.5 1.0
O C:MET196 4.9 25.1 1.0
N4 C:OS6307 5.0 21.9 1.0
CB C:THR93 5.0 26.1 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 Jul 27 21:59:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy