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Chlorine in PDB 4m5h: 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: 4m5h 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) 32.31 / 1.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.775, 57.588, 38.464, 90.00, 115.41, 90.00
R / Rfree (%) 13.4 / 14.9

Other elements in 4m5h:

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) 4 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 4m5h). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 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: 4m5h:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4m5h

Go back to Chlorine Binding Sites List in 4m5h
Chlorine binding site 1 out of 3 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:Cl307

b:18.0
occ:1.00
 O A:HOH547 2.8 25.7 1.0
OG A:SER13 2.9 12.8 0.3
O A:HOH494 3.1 16.3 1.0
N A:LEU15 3.2 7.8 1.0
C A:SER13 3.5 8.8 1.0
N A:PRO14 3.5 8.1 1.0
CA A:SER13 3.5 9.8 0.3
CA A:SER13 3.5 9.2 0.7
CB A:LEU15 3.6 9.6 1.0
CD A:PRO14 3.7 8.5 1.0
CB A:SER13 3.8 11.5 0.3
CB A:SER13 3.8 10.2 0.7
CA A:LEU15 4.0 8.4 1.0
O A:SER13 4.0 8.4 1.0
CZ2 A:TRP158 4.1 12.0 1.0
C A:PRO14 4.2 6.9 1.0
CA A:PRO14 4.3 7.4 1.0
N A:GLU16 4.4 8.8 1.0
OG A:SER13 4.5 11.4 0.7
O A:HOH604 4.7 30.8 1.0
CB A:PRO14 4.7 8.0 1.0
C A:LEU15 4.8 8.5 1.0
CG A:PRO14 4.8 8.5 1.0
CE2 A:TRP158 4.9 12.4 1.0
N A:SER13 4.9 9.2 1.0
NE1 A:TRP158 4.9 13.7 1.0
O A:HOH607 4.9 31.0 1.0
CG A:LEU15 4.9 10.8 1.0
CH2 A:TRP158 5.0 11.9 1.0

Chlorine binding site 2 out of 3 in 4m5h

Go back to Chlorine Binding Sites List in 4m5h
Chlorine binding site 2 out of 3 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:Cl308

b:11.5
occ:1.00
 O A:HOH503 3.0 20.5 1.0
O A:HOH468 3.1 18.5 1.0
O A:HOH506 3.4 21.9 1.0
CG A:ASP139 3.4 8.8 1.0
OD1 A:ASP139 3.4 7.8 1.0
NZ A:LYS119 3.4 9.0 1.0
N A:ASP139 3.6 7.0 1.0
CD A:PRO138 3.7 6.9 1.0
CB A:ASP139 3.7 8.4 1.0
OD2 A:ASP139 3.7 10.4 1.0
CB A:PHE137 3.8 6.3 1.0
CE A:LYS119 3.8 8.7 1.0
CG A:PRO114 3.9 7.9 1.0
N A:PRO138 4.0 6.5 1.0
CD2 A:PHE137 4.3 6.6 1.0
CA A:ASP139 4.3 7.5 1.0
O A:HOH594 4.3 29.3 1.0
CB A:PRO138 4.4 7.2 1.0
CG A:PHE137 4.4 5.9 1.0
CG A:PRO138 4.4 7.5 1.0
C A:PRO138 4.5 6.8 1.0
CA A:PRO138 4.6 6.5 1.0
C A:PHE137 4.6 6.2 1.0
CB A:PRO114 4.6 7.2 1.0
CD A:PRO114 4.7 8.0 1.0
CA A:PHE137 4.7 6.1 1.0
O A:HOH536 4.9 23.4 1.0

Chlorine binding site 3 out of 3 in 4m5h

Go back to Chlorine Binding Sites List in 4m5h
Chlorine binding site 3 out of 3 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:Cl309

b:13.6
occ:1.00
 O A:HOH628 2.5 30.3 1.0
O A:HOH508 2.8 23.7 1.0
N A:VAL83 3.2 11.7 1.0
N A:THR93 3.3 6.2 1.0
CA A:ARG92 3.5 6.8 1.0
CA A:ARG82 3.6 9.4 1.0
CG2 A:THR93 3.8 9.9 1.0
O A:VAL83 3.8 16.2 1.0
OG1 A:THR93 3.9 9.0 1.0
C A:ARG92 3.9 6.0 1.0
C A:ARG82 3.9 10.2 1.0
CG A:ARG82 4.0 11.3 1.0
O A:GLY81 4.0 11.4 1.0
CB A:ARG92 4.0 8.0 1.0
O A:HOH513 4.0 34.0 1.0
CD1 A:LEU11 4.0 8.2 1.0
O A:PRO91 4.2 7.2 1.0
CB A:THR93 4.2 8.8 1.0
CA A:VAL83 4.2 14.1 1.0
CB A:ARG82 4.3 9.7 1.0
CA A:THR93 4.3 6.6 1.0
CB A:VAL83 4.5 17.5 1.0
C A:VAL83 4.5 14.1 1.0
N A:ARG82 4.5 9.0 1.0
C A:GLY81 4.6 10.2 1.0
N A:ARG92 4.6 6.1 1.0
O A:HOH535 4.7 21.5 1.0
C A:PRO91 4.8 6.2 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: Sun Jul 21 19:34:47 2024

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