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Chlorine in PDB 4m5g: The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase

Enzymatic activity of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase

All present enzymatic activity of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase:
2.7.6.3;

Protein crystallography data

The structure of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase, PDB code: 4m5g was solved by M.Yun, D.Hoagland, G.Kumar, B.Waddell, C.O.Rock, R.E.Lee, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.20 / 1.31
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.875, 57.417, 38.327, 90.00, 113.96, 90.00
R / Rfree (%) 14.4 / 17.7

Other elements in 4m5g:

The structure of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase (pdb code 4m5g). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase, PDB code: 4m5g:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4m5g

Go back to Chlorine Binding Sites List in 4m5g
Chlorine binding site 1 out of 4 in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:18.6
occ:1.00
 O A:HOH513 3.0 23.9 1.0
O A:HOH438 3.2 17.9 1.0
N A:LEU15 3.3 9.3 1.0
C A:SER13 3.5 11.1 1.0
N A:PRO14 3.5 10.3 1.0
CA A:SER13 3.5 12.9 1.0
CB A:LEU15 3.6 10.3 1.0
CD A:PRO14 3.7 11.6 1.0
CB A:SER13 3.8 15.2 1.0
O A:SER13 4.0 11.5 1.0
CA A:LEU15 4.0 9.3 1.0
CZ2 A:TRP158 4.0 13.3 1.0
C A:PRO14 4.2 9.1 1.0
CA A:PRO14 4.3 9.6 1.0
N A:GLU16 4.5 9.9 1.0
O A:HOH545 4.5 43.5 1.0
OG A:SER13 4.5 18.2 1.0
CB A:PRO14 4.6 9.9 1.0
O A:HOH439 4.7 28.6 1.0
O A:HOH440 4.8 34.4 1.0
NE1 A:TRP158 4.8 14.0 1.0
CG A:PRO14 4.8 11.1 1.0
CE2 A:TRP158 4.8 13.0 1.0
N A:SER13 4.9 13.5 1.0
C A:LEU15 4.9 9.3 1.0
CH2 A:TRP158 5.0 13.0 1.0
CG A:LEU15 5.0 11.8 1.0

Chlorine binding site 2 out of 4 in 4m5g

Go back to Chlorine Binding Sites List in 4m5g
Chlorine binding site 2 out of 4 in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:12.4
occ:1.00
 O A:HOH500 3.0 23.7 1.0
O A:HOH499 3.2 27.7 1.0
NZ A:LYS119 3.3 16.1 1.0
CG A:ASP139 3.3 9.7 1.0
OD1 A:ASP139 3.4 9.1 1.0
N A:ASP139 3.5 7.5 1.0
CB A:ASP139 3.6 9.1 1.0
CD A:PRO138 3.6 8.4 1.0
CB A:PHE137 3.7 8.2 1.0
OD2 A:ASP139 3.7 11.3 1.0
CE A:LYS119 3.8 13.5 1.0
CG A:PRO114 3.8 8.6 1.0
N A:PRO138 3.9 7.6 1.0
CA A:ASP139 4.2 7.9 1.0
CB A:PRO138 4.3 9.7 1.0
CD2 A:PHE137 4.3 8.3 1.0
CG A:PRO138 4.3 9.4 1.0
CG A:PHE137 4.4 8.1 1.0
C A:PRO138 4.4 7.3 1.0
CA A:PRO138 4.4 8.1 1.0
C A:PHE137 4.5 7.2 1.0
O A:HOH563 4.5 30.5 1.0
CD A:PRO114 4.6 8.5 1.0
CB A:PRO114 4.6 7.7 1.0
CA A:PHE137 4.7 7.8 1.0

Chlorine binding site 3 out of 4 in 4m5g

Go back to Chlorine Binding Sites List in 4m5g
Chlorine binding site 3 out of 4 in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:18.6
occ:1.00
 O A:HOH406 3.0 15.4 1.0
O A:HOH408 3.1 25.5 1.0
N A:GLY122 3.2 6.1 1.0
CD1 A:PHE152 3.7 15.8 1.0
O A:HOH407 3.8 19.6 1.0
CD1 A:LEU45 3.8 17.7 1.0
CA A:GLY122 3.9 6.5 1.0
O A:ASN120 3.9 8.2 1.0
CA A:ARG121 4.1 5.8 1.0
C A:ARG121 4.1 5.6 1.0
CE1 A:PHE152 4.2 16.7 1.0
C A:ASN120 4.7 7.0 1.0
CG A:LEU45 4.7 17.2 1.0
CD2 A:LEU45 4.8 18.7 1.0
N A:ARG121 4.8 5.8 1.0
CG A:PHE152 4.8 15.7 1.0
N A:PHE123 4.9 6.5 1.0
C A:GLY122 5.0 6.2 1.0

Chlorine binding site 4 out of 4 in 4m5g

Go back to Chlorine Binding Sites List in 4m5g
Chlorine binding site 4 out of 4 in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:23.5
occ:1.00
 N A:THR93 3.3 9.5 1.0
O A:GLY81 3.6 22.1 1.0
N A:VAL83 3.6 28.3 1.0
CA A:ARG92 3.6 10.3 1.0
CG2 A:THR93 3.7 14.2 1.0
OG1 A:THR93 3.7 15.4 1.0
CA A:ARG82 3.8 21.0 1.0
CB A:ARG92 3.9 13.1 1.0
C A:ARG92 4.0 9.5 1.0
CB A:THR93 4.1 13.1 1.0
C A:ARG82 4.2 24.1 1.0
CD A:ARG82 4.3 19.3 1.0
CA A:THR93 4.3 9.6 1.0
CD1 A:LEU11 4.3 12.1 1.0
C A:GLY81 4.4 20.7 1.0
O A:VAL83 4.4 35.4 1.0
O A:PRO91 4.4 10.0 1.0
O A:HOH550 4.5 38.7 1.0
N A:ARG82 4.5 19.9 1.0
CA A:VAL83 4.7 32.8 1.0
CB A:ARG82 4.8 19.2 1.0
N A:ARG92 4.8 9.2 1.0
CG A:ARG82 4.9 19.5 1.0
CB A:VAL83 4.9 34.6 1.0

Reference:

M.K.Yun, D.Hoagland, G.Kumar, M.B.Waddell, C.O.Rock, R.E.Lee, S.W.White. The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase. Bioorg.Med.Chem. V. 22 2157 2014.
ISSN: ISSN 0968-0896
PubMed: 24613625
DOI: 10.1016/J.BMC.2014.02.022
Page generated: Fri Jul 11 18:56:15 2025

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