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Chlorine in PDB 2ynd: Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.:
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor., PDB code: 2ynd was solved by M.H.Wright, B.Clough, M.D.Rackham, J.A.Brannigan, M.Grainger, A.R.Bottrill, W.P.Heal, M.Broncel, R.A.Serwa, D.Mann, R.J.Leatherbarrow, A.J.Wilkinson, A.A.Holder, E.W.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.60 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.450, 119.050, 176.730, 90.00, 90.00, 90.00
R / Rfree (%) 16.768 / 22.316

Other elements in 2ynd:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. (pdb code 2ynd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor., PDB code: 2ynd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 2ynd

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Chlorine binding site 1 out of 9 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:36.2
occ:1.00
 CLF A:6461001 0.0 36.2 1.0
CAW A:6461001 1.8 30.1 1.0
CAJ A:6461001 2.7 29.7 1.0
CBC A:6461001 2.8 27.7 1.0
NAT A:6461001 3.1 23.1 1.0
O A:HOH2270 3.2 29.2 1.0
SBF A:6461001 3.2 24.8 1.0
OAE A:6461001 3.3 24.8 1.0
O A:HOH2444 3.8 27.0 1.0
CAB A:6461001 3.8 19.0 1.0
CAZ A:6461001 4.0 32.3 1.0
CAX A:6461001 4.0 28.4 1.0
CBB A:6461001 4.1 20.9 1.0
CAV A:6461001 4.2 20.5 1.0
O A:ASP385 4.4 22.3 1.0
CAK A:6461001 4.5 29.7 1.0
CB A:ASP385 4.6 26.7 1.0
OAD A:6461001 4.7 22.6 1.0
N A:ASP385 4.9 24.9 1.0

Chlorine binding site 2 out of 9 in 2ynd

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Chlorine binding site 2 out of 9 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:31.6
occ:1.00
 CLG A:6461001 0.0 31.6 1.0
CAX A:6461001 1.8 28.4 1.0
CAK A:6461001 2.6 29.7 1.0
OAD A:6461001 2.7 22.6 1.0
CBC A:6461001 2.8 27.7 1.0
OH A:TYR334 3.0 17.3 1.0
SBF A:6461001 3.3 24.8 1.0
O A:HOH2397 3.6 16.1 1.0
CZ A:TYR334 3.7 15.2 1.0
ND2 A:ASN365 3.7 14.8 1.0
CE2 A:TYR334 3.7 14.7 1.0
CAZ A:6461001 3.9 32.3 1.0
CAW A:6461001 4.0 30.1 1.0
CE1 A:HIS213 4.0 15.6 1.0
CG A:ASN365 4.1 13.1 1.0
CZ A:PHE105 4.4 19.7 1.0
OAE A:6461001 4.4 24.8 1.0
CE1 A:PHE105 4.5 16.8 1.0
CAJ A:6461001 4.5 29.7 1.0
NAT A:6461001 4.5 23.1 1.0
OD1 A:ASN365 4.6 12.3 1.0
ND1 A:HIS213 4.6 15.5 1.0
CG A:TYR211 4.6 18.0 1.0
CD2 A:TYR211 4.6 17.7 1.0
CBB A:6461001 4.6 20.9 1.0
CE2 A:TYR211 4.7 19.1 1.0
CD1 A:TYR211 4.7 19.2 1.0
CB A:ASN365 4.7 12.5 1.0
CZ A:TYR211 4.8 21.5 1.0
O A:HOH2391 4.8 19.2 1.0
CE1 A:TYR211 4.8 20.6 1.0
CD2 A:TYR334 4.9 12.6 1.0
CE1 A:TYR334 4.9 13.3 1.0
CAU A:6461001 5.0 19.5 1.0

Chlorine binding site 3 out of 9 in 2ynd

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Chlorine binding site 3 out of 9 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1416

b:13.3
occ:1.00
 NZ A:LYS180 3.1 10.3 1.0
O A:HOH2071 3.1 11.8 1.0
CE1 A:TYR65 3.8 13.6 1.0
O A:HOH2070 3.8 8.5 1.0
CD A:LYS180 3.9 10.2 1.0
CE A:LYS180 4.0 10.3 1.0
OH A:TYR65 4.5 12.5 1.0
CD1 A:TYR65 4.6 14.5 1.0
CZ A:TYR65 4.6 13.9 1.0

Chlorine binding site 4 out of 9 in 2ynd

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Chlorine binding site 4 out of 9 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1001

b:27.6
occ:1.00
 CLF B:6461001 0.0 27.6 1.0
CAW B:6461001 1.8 25.6 1.0
CAJ B:6461001 2.7 26.4 1.0
CBC B:6461001 2.8 23.9 1.0
O B:HOH2420 3.0 29.7 1.0
OAE B:6461001 3.1 22.6 1.0
NAT B:6461001 3.2 21.6 1.0
O B:HOH2135 3.2 23.6 1.0
SBF B:6461001 3.2 22.3 1.0
O B:HOH2240 3.3 39.7 1.0
CAB B:6461001 3.8 16.2 1.0
O B:HOH2398 3.8 28.2 1.0
CAZ B:6461001 4.0 28.0 1.0
O B:ASP385 4.0 27.8 1.0
CAX B:6461001 4.1 25.5 1.0
CBB B:6461001 4.1 18.4 1.0
CAV B:6461001 4.2 18.9 1.0
OD2 B:ASP385 4.3 44.9 1.0
CB B:ASP385 4.3 32.8 1.0
CAK B:6461001 4.5 27.3 1.0
N B:ASP385 4.7 25.6 1.0
OAD B:6461001 4.7 20.5 1.0
CG B:ASP385 4.7 37.0 1.0
C B:ASP385 4.8 28.5 1.0
CA B:ASP385 4.9 27.9 1.0

Chlorine binding site 5 out of 9 in 2ynd

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Chlorine binding site 5 out of 9 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1001

b:30.2
occ:1.00
 CLG B:6461001 0.0 30.2 1.0
CAX B:6461001 1.8 25.5 1.0
CAK B:6461001 2.7 27.3 1.0
OAD B:6461001 2.7 20.5 1.0
CBC B:6461001 2.9 23.9 1.0
OH B:TYR334 3.0 14.7 1.0
SBF B:6461001 3.4 22.3 1.0
ND2 B:ASN365 3.5 16.6 1.0
O B:HOH2359 3.7 16.7 1.0
CE2 B:TYR334 3.7 12.4 1.0
CZ B:TYR334 3.7 13.2 1.0
CE1 B:HIS213 4.0 18.7 1.0
CAZ B:6461001 4.0 28.0 1.0
CG B:ASN365 4.0 17.1 1.0
CAW B:6461001 4.1 25.6 1.0
OAE B:6461001 4.4 22.6 1.0
CZ B:PHE105 4.4 18.0 1.0
CE1 B:PHE105 4.5 17.9 1.0
OD1 B:ASN365 4.5 17.7 1.0
NAT B:6461001 4.5 21.6 1.0
CG B:TYR211 4.5 13.9 1.0
ND1 B:HIS213 4.5 15.9 1.0
CAJ B:6461001 4.6 26.4 1.0
CD1 B:TYR211 4.6 14.6 1.0
CD2 B:TYR211 4.6 14.6 1.0
CB B:ASN365 4.6 14.5 1.0
CE2 B:TYR211 4.6 16.0 1.0
CE1 B:TYR211 4.7 13.8 1.0
CBB B:6461001 4.7 18.4 1.0
CZ B:TYR211 4.7 14.7 1.0
CD2 B:TYR334 4.9 12.6 1.0
O B:HOH2340 4.9 11.8 1.0
CE1 B:TYR334 4.9 12.4 1.0
CAU B:6461001 5.0 19.1 1.0

Chlorine binding site 6 out of 9 in 2ynd

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Chlorine binding site 6 out of 9 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1415

b:13.1
occ:1.00
 O B:HOH2060 3.2 18.5 1.0
NZ B:LYS180 3.2 11.2 1.0
CE2 B:TYR65 3.8 13.5 1.0
CD B:LYS180 3.9 12.1 1.0
CE B:LYS180 4.1 11.9 1.0
CD2 B:TYR65 4.5 13.6 1.0
OH B:TYR65 4.7 18.2 1.0
CZ B:TYR65 4.7 14.6 1.0
O B:HOH2214 4.9 18.1 1.0

Chlorine binding site 7 out of 9 in 2ynd

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Chlorine binding site 7 out of 9 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1001

b:40.1
occ:1.00
 CLF C:6461001 0.0 40.1 1.0
CAW C:6461001 1.8 43.2 1.0
CBC C:6461001 2.7 44.3 1.0
CAJ C:6461001 2.7 44.2 1.0
NAT C:6461001 2.8 35.0 1.0
OAE C:6461001 2.8 49.7 1.0
SBF C:6461001 2.9 46.2 1.0
O C:HOH2377 3.2 34.8 1.0
CAB C:6461001 3.6 23.9 1.0
CBB C:6461001 3.8 28.4 1.0
CAV C:6461001 3.9 25.4 1.0
CAX C:6461001 4.0 44.9 1.0
CAZ C:6461001 4.0 50.0 1.0
OAD C:6461001 4.4 45.8 1.0
CB C:ASP385 4.4 34.4 1.0
CAK C:6461001 4.5 46.0 1.0
CB C:ASP98 4.7 29.8 1.0

Chlorine binding site 8 out of 9 in 2ynd

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Chlorine binding site 8 out of 9 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1001

b:43.4
occ:1.00
 CLG C:6461001 0.0 43.4 1.0
CAX C:6461001 1.8 44.9 1.0
CAK C:6461001 2.7 46.0 1.0
CBC C:6461001 2.7 44.3 1.0
OAD C:6461001 2.8 45.8 1.0
OH C:TYR334 3.2 18.2 1.0
SBF C:6461001 3.3 46.2 1.0
CE2 C:TYR334 3.6 16.5 1.0
O C:HOH2321 3.8 24.1 1.0
CZ C:TYR334 3.8 18.0 1.0
ND2 C:ASN365 3.9 16.6 1.0
CAW C:6461001 4.0 43.2 1.0
CAZ C:6461001 4.0 50.0 1.0
CE1 C:HIS213 4.1 12.3 0.5
CG C:ASN365 4.1 15.8 1.0
CE1 C:TYR211 4.3 33.9 1.0
CZ C:TYR211 4.3 33.7 1.0
CD1 C:TYR211 4.3 31.6 1.0
O C:HOH2238 4.3 28.1 1.0
OAE C:6461001 4.3 49.7 1.0
NAT C:6461001 4.4 35.0 1.0
OD1 C:ASN365 4.4 15.3 1.0
ND1 C:HIS213 4.4 12.4 0.5
CBB C:6461001 4.5 28.4 1.0
CE2 C:TYR211 4.5 34.0 1.0
CG C:TYR211 4.5 29.7 1.0
CAJ C:6461001 4.5 44.2 1.0
CD2 C:TYR211 4.6 33.1 1.0
CB C:ASN365 4.6 13.6 1.0
CE1 C:PHE105 4.7 17.4 1.0
CZ C:PHE105 4.8 19.6 1.0
CAU C:6461001 4.8 28.6 1.0
OH C:TYR211 4.9 36.0 1.0
CD2 C:TYR334 4.9 15.4 1.0

Chlorine binding site 9 out of 9 in 2ynd

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Chlorine binding site 9 out of 9 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1415

b:12.7
occ:1.00
 O C:HOH2084 3.0 14.0 1.0
NZ C:LYS180 3.3 8.6 1.0
CE2 C:TYR65 3.6 14.3 1.0
O C:HOH2069 3.7 16.8 1.0
CD C:LYS180 3.8 9.4 1.0
CE C:LYS180 4.1 9.0 1.0
CD2 C:TYR65 4.4 12.9 1.0
OH C:TYR65 4.5 14.5 1.0
CZ C:TYR65 4.5 14.4 1.0

Reference:

M.H.Wright, B.Clough, M.D.Rackham, K.Rangachari, J.A.Brannigan, M.Grainger, D.K.Moss, A.R.Bottrill, W.P.Heal, M.Broncel, R.A.Serwa, D.Brady, D.Mann, R.J.Leatherbarrow, R.Tewari, A.J.Wilkinson, A.A.Holder, E.W.Tate. Validation of N-Myristoyltransferase As An Antimalarial Drug Target Using An Integrated Chemical Biology Approach. Nat.Chem. V. 6 112 2014.
ISSN: ISSN 1755-4330
PubMed: 24451586
DOI: 10.1038/NCHEM.1836
Page generated: Sat Jul 20 15:11:22 2024

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