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Chlorine in PDB 2wd8: Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204

Enzymatic activity of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204

All present enzymatic activity of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204:
1.5.1.33;

Protein crystallography data

The structure of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204, PDB code: 2wd8 was solved by D.A.Robinson, P.G.Wyatt, D.Spinks, R.Brenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.640, 89.801, 83.061, 90.00, 115.55, 90.00
R / Rfree (%) 15.844 / 22.622

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 (pdb code 2wd8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204, PDB code: 2wd8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 2wd8

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Chlorine binding site 1 out of 10 in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1269

b:52.7
occ:1.00
 N A:ARG14 3.2 32.4 1.0
CB A:LYS13 3.3 32.8 1.0
CA A:LYS13 3.5 32.2 1.0
C A:LYS13 3.8 32.0 1.0
O A:HOH2008 4.0 30.2 1.0
CA A:ARG14 4.2 32.5 1.0
CD A:ARG17 4.3 28.9 1.0
CG A:LYS13 4.6 33.5 1.0
O A:ALA12 4.8 31.6 1.0
CG A:ARG14 4.8 31.5 1.0
N A:LYS13 4.9 31.7 1.0
CB A:ARG17 4.9 28.6 1.0

Chlorine binding site 2 out of 10 in 2wd8

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Chlorine binding site 2 out of 10 in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1270

b:26.5
occ:1.00
 CLAC A:VGF1270 0.0 26.5 1.0
CAS A:VGF1270 1.7 27.6 1.0
CAN A:VGF1270 2.7 26.8 1.0
CAR A:VGF1270 2.7 27.1 1.0
CLAB A:VGF1270 3.1 29.0 1.0
CG2 A:VAL206 3.2 35.5 1.0
O A:TRP221 3.3 32.6 1.0
CE3 A:TRP221 3.6 35.5 1.0
CB A:TRP221 3.7 32.4 1.0
C A:TRP221 3.9 32.2 1.0
CD2 A:LEU263 3.9 27.1 1.0
CA A:TRP221 4.0 32.1 1.0
CAK A:VGF1270 4.0 27.2 1.0
CAQ A:VGF1270 4.0 27.9 1.0
CD1 A:LEU263 4.1 23.4 1.0
O A:HOH2122 4.2 44.2 1.0
CD2 A:TRP221 4.3 34.4 1.0
CD A:LYS224 4.3 29.4 1.0
CB A:LYS224 4.4 30.8 1.0
CB A:VAL206 4.4 33.2 1.0
CG A:TRP221 4.4 33.2 1.0
CAJ A:VGF1270 4.5 28.2 1.0
CZ3 A:TRP221 4.6 34.1 1.0
CG1 A:VAL206 4.6 33.4 1.0
CG A:LEU263 4.6 26.9 1.0
CG A:LYS224 5.0 30.0 1.0
N A:ARG222 5.0 31.9 1.0

Chlorine binding site 3 out of 10 in 2wd8

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Chlorine binding site 3 out of 10 in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1270

b:29.0
occ:1.00
 CLAB A:VGF1270 0.0 29.0 1.0
CAR A:VGF1270 1.7 27.1 1.0
CAS A:VGF1270 2.7 27.6 1.0
CAK A:VGF1270 2.7 27.2 1.0
CLAC A:VGF1270 3.1 26.5 1.0
ND1 D:HIS267 3.4 26.5 1.0
OXT D:ALA268 3.6 27.1 1.0
CZ3 A:TRP221 3.9 34.1 1.0
CD A:LYS224 3.9 29.4 1.0
CG D:HIS267 3.9 26.8 1.0
CE3 A:TRP221 3.9 35.5 1.0
CB D:HIS267 4.0 25.8 1.0
CAN A:VGF1270 4.0 26.8 1.0
CAJ A:VGF1270 4.0 28.2 1.0
CD1 A:LEU263 4.1 23.4 1.0
N D:ALA268 4.1 26.3 1.0
CB D:ALA268 4.2 25.6 1.0
CE1 D:HIS267 4.2 27.5 1.0
C D:ALA268 4.3 26.8 1.0
CE A:MET163 4.4 24.6 0.8
CA D:ALA268 4.4 26.4 1.0
CD2 A:LEU263 4.4 27.1 1.0
CAQ A:VGF1270 4.5 27.9 1.0
CG A:LEU263 4.6 26.9 1.0
C D:HIS267 4.7 27.0 1.0
O D:HOH2162 4.7 28.4 1.0
CD2 D:HIS267 4.8 25.9 1.0
CB A:LYS224 4.8 30.8 1.0
CE A:LYS224 4.8 27.7 1.0
CA D:HIS267 4.9 26.5 1.0
CG A:LYS224 5.0 30.0 1.0
NE2 D:HIS267 5.0 28.4 1.0

Chlorine binding site 4 out of 10 in 2wd8

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Chlorine binding site 4 out of 10 in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1269

b:27.8
occ:1.00
 CLAC B:VGF1269 0.0 27.8 1.0
CAS B:VGF1269 1.7 28.6 1.0
CAN B:VGF1269 2.7 28.9 1.0
CAR B:VGF1269 2.7 28.9 1.0
CLAB B:VGF1269 3.2 30.3 1.0
O B:TRP221 3.3 31.5 1.0
CG2 B:VAL206 3.5 33.7 1.0
CB B:TRP221 3.6 32.3 1.0
CE3 B:TRP221 3.6 34.0 1.0
CA B:TRP221 3.8 32.4 1.0
CD2 B:LEU263 3.8 26.1 1.0
C B:TRP221 3.9 31.7 1.0
CD1 B:LEU263 4.0 24.9 1.0
CAQ B:VGF1269 4.0 28.2 1.0
CAK B:VGF1269 4.0 29.2 1.0
CG1 B:VAL206 4.1 33.8 1.0
CD2 B:TRP221 4.3 33.7 1.0
CD B:LYS224 4.3 34.0 1.0
CG B:TRP221 4.3 33.0 1.0
CB B:VAL206 4.4 34.0 1.0
CB B:LYS224 4.5 33.0 1.0
CAJ B:VGF1269 4.5 29.1 1.0
CG B:LEU263 4.5 26.8 1.0
CZ3 B:TRP221 4.6 33.8 1.0
CG B:LYS224 5.0 33.6 1.0

Chlorine binding site 5 out of 10 in 2wd8

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Chlorine binding site 5 out of 10 in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1269

b:30.3
occ:1.00
 CLAB B:VGF1269 0.0 30.3 1.0
CAR B:VGF1269 1.7 28.9 1.0
CAK B:VGF1269 2.7 29.2 1.0
CAS B:VGF1269 2.7 28.6 1.0
CLAC B:VGF1269 3.2 27.8 1.0
ND1 C:HIS267 3.4 23.7 1.0
OXT C:ALA268 3.6 25.2 1.0
CD B:LYS224 3.7 34.0 1.0
CE3 B:TRP221 4.0 34.0 1.0
CAJ B:VGF1269 4.0 29.1 1.0
CZ3 B:TRP221 4.0 33.8 1.0
CG C:HIS267 4.0 23.3 1.0
CAN B:VGF1269 4.0 28.9 1.0
CD1 B:LEU263 4.0 24.9 1.0
CE1 C:HIS267 4.1 22.9 1.0
N C:ALA268 4.1 23.8 1.0
CB C:ALA268 4.2 24.6 1.0
CB C:HIS267 4.2 22.9 1.0
C C:ALA268 4.2 24.9 1.0
CE B:MET163 4.3 29.7 1.0
CA C:ALA268 4.4 24.6 1.0
CD2 B:LEU263 4.4 26.1 1.0
CAQ B:VGF1269 4.5 28.2 1.0
CG B:LEU263 4.6 26.8 1.0
CE B:LYS224 4.6 34.9 1.0
CB B:LYS224 4.7 33.0 1.0
C C:HIS267 4.8 23.4 1.0
CG B:LYS224 4.8 33.6 1.0
O B:HOH2194 4.9 22.8 1.0
CD2 C:HIS267 4.9 24.7 1.0
NE2 C:HIS267 4.9 23.5 1.0

Chlorine binding site 6 out of 10 in 2wd8

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Chlorine binding site 6 out of 10 in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1269

b:61.7
occ:1.00
 CB C:HIS35 3.4 32.4 1.0
CE1 C:HIS33 3.6 24.2 1.0
O C:HOH2078 4.1 45.7 1.0
O C:HOH2076 4.1 43.0 1.0
CB C:ALA94 4.1 30.8 1.0
CG C:HIS35 4.2 36.3 1.0
ND1 C:HIS35 4.2 39.8 1.0
N C:HIS35 4.4 30.1 1.0
CB C:LEU63 4.4 37.1 1.0
NE2 C:HIS33 4.4 24.4 1.0
CG C:LEU63 4.5 36.3 1.0
CA C:HIS35 4.5 32.1 1.0
ND1 C:HIS33 4.5 23.8 1.0
N C:LEU63 4.6 37.5 1.0
O C:ALA61 4.7 33.2 1.0
O C:HOH2031 4.7 41.0 1.0
CD1 C:LEU63 4.8 33.2 1.0
O C:HOH2022 4.8 46.8 1.0

Chlorine binding site 7 out of 10 in 2wd8

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Chlorine binding site 7 out of 10 in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1270

b:33.2
occ:1.00
 CLAC C:VGF1270 0.0 33.2 1.0
CAS C:VGF1270 1.7 34.4 1.0
CAR C:VGF1270 2.7 33.7 1.0
CAN C:VGF1270 2.8 33.7 1.0
CLAB C:VGF1270 3.1 33.9 1.0
O C:TRP221 3.2 39.0 1.0
CE3 C:TRP221 3.4 43.8 1.0
CG2 C:VAL206 3.7 43.6 1.0
CB C:TRP221 3.8 41.2 1.0
C C:TRP221 3.9 39.8 1.0
CD2 C:LEU263 3.9 25.8 1.0
CA C:TRP221 4.0 40.8 1.0
CAK C:VGF1270 4.0 33.1 1.0
CD1 C:LEU263 4.0 23.4 1.0
CAQ C:VGF1270 4.1 33.0 1.0
CG1 C:VAL206 4.1 43.0 1.0
CD2 C:TRP221 4.2 43.5 1.0
CD C:LYS224 4.2 29.4 1.0
CZ3 C:TRP221 4.3 43.2 1.0
CB C:LYS224 4.4 30.7 1.0
CG C:TRP221 4.5 42.5 1.0
CB C:VAL206 4.5 43.5 1.0
CAJ C:VGF1270 4.5 32.4 1.0
CG C:LEU263 4.6 25.1 1.0
CG C:LYS224 5.0 30.6 1.0

Chlorine binding site 8 out of 10 in 2wd8

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Chlorine binding site 8 out of 10 in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1270

b:33.9
occ:1.00
 CLAB C:VGF1270 0.0 33.9 1.0
CAR C:VGF1270 1.7 33.7 1.0
CAK C:VGF1270 2.7 33.1 1.0
CAS C:VGF1270 2.7 34.4 1.0
CLAC C:VGF1270 3.1 33.2 1.0
ND1 B:HIS267 3.4 28.2 1.0
OXT B:ALA268 3.5 29.9 1.0
CZ3 C:TRP221 3.6 43.2 1.0
CE3 C:TRP221 3.8 43.8 1.0
CD C:LYS224 3.9 29.4 1.0
CG B:HIS267 3.9 26.7 1.0
CAJ C:VGF1270 4.0 32.4 1.0
CD1 C:LEU263 4.0 23.4 1.0
N B:ALA268 4.0 28.5 1.0
CB B:HIS267 4.0 27.2 1.0
CAN C:VGF1270 4.0 33.7 1.0
CE1 B:HIS267 4.2 28.4 1.0
C B:ALA268 4.2 29.9 1.0
CB B:ALA268 4.3 29.1 1.0
CA B:ALA268 4.4 29.1 1.0
CD2 C:LEU263 4.5 25.8 1.0
CE C:MET163 4.5 29.5 1.0
CAQ C:VGF1270 4.5 33.0 1.0
CG C:LEU263 4.6 25.1 1.0
C B:HIS267 4.7 28.1 1.0
CE C:LYS224 4.8 28.1 1.0
O C:HOH2172 4.8 25.7 1.0
CD2 B:HIS267 4.8 25.9 1.0
CB C:LYS224 4.9 30.7 1.0
CA B:HIS267 4.9 27.6 1.0
CH2 C:TRP221 5.0 43.0 1.0
NE2 B:HIS267 5.0 29.1 1.0
CG C:LYS224 5.0 30.6 1.0

Chlorine binding site 9 out of 10 in 2wd8

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Chlorine binding site 9 out of 10 in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1269

b:27.9
occ:1.00
 CLAC D:VGF1269 0.0 27.9 1.0
CAS D:VGF1269 1.7 26.3 1.0
CAR D:VGF1269 2.7 26.6 1.0
CAN D:VGF1269 2.7 27.0 1.0
CLAB D:VGF1269 3.0 26.3 1.0
CG2 D:VAL206 3.3 37.6 1.0
O D:TRP221 3.3 30.8 1.0
CE3 D:TRP221 3.5 37.2 1.0
CD2 D:LEU263 3.7 25.4 1.0
CB D:TRP221 3.7 33.2 1.0
C D:TRP221 3.9 31.8 1.0
CA D:TRP221 3.9 32.6 1.0
CAK D:VGF1269 4.0 25.4 1.0
CAQ D:VGF1269 4.0 25.8 1.0
CD1 D:LEU263 4.0 23.3 1.0
CD2 D:TRP221 4.2 36.3 1.0
CD D:LYS224 4.2 26.9 1.0
CG D:TRP221 4.4 34.6 1.0
CB D:LYS224 4.4 27.2 1.0
CZ3 D:TRP221 4.4 35.7 1.0
CAJ D:VGF1269 4.4 25.3 1.0
CG D:LEU263 4.5 26.3 1.0
CB D:VAL206 4.5 37.4 1.0
CG1 D:VAL206 4.6 36.8 1.0
CG D:LYS224 4.9 28.4 1.0
O D:HOH2119 4.9 44.2 1.0

Chlorine binding site 10 out of 10 in 2wd8

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Chlorine binding site 10 out of 10 in the Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Pteridine Reductase 1 (PTR1) From Trypanosoma Brucei in Complex with Nadp and DDD00071204 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1269

b:26.3
occ:1.00
 CLAB D:VGF1269 0.0 26.3 1.0
CAR D:VGF1269 1.7 26.6 1.0
CAS D:VGF1269 2.7 26.3 1.0
CAK D:VGF1269 2.8 25.4 1.0
CLAC D:VGF1269 3.0 27.9 1.0
ND1 A:HIS267 3.4 28.0 1.0
OXT A:ALA268 3.5 29.9 1.0
CZ3 D:TRP221 3.6 35.7 1.0
CD D:LYS224 3.7 26.9 1.0
CE3 D:TRP221 3.7 37.2 1.0
CG A:HIS267 4.0 27.0 1.0
CAN D:VGF1269 4.0 27.0 1.0
CAJ D:VGF1269 4.0 25.3 1.0
N A:ALA268 4.1 28.4 1.0
CB A:HIS267 4.1 27.8 1.0
CD1 D:LEU263 4.2 23.3 1.0
CE1 A:HIS267 4.2 26.3 1.0
C A:ALA268 4.3 29.1 1.0
CB A:ALA268 4.3 29.2 1.0
CD2 D:LEU263 4.3 25.4 1.0
CA A:ALA268 4.4 29.2 1.0
CE D:MET163 4.5 30.1 1.0
CAQ D:VGF1269 4.6 25.8 1.0
CG D:LEU263 4.6 26.3 1.0
CE D:LYS224 4.7 27.5 1.0
CB D:LYS224 4.7 27.2 1.0
C A:HIS267 4.7 28.1 1.0
CG D:LYS224 4.8 28.4 1.0
CD2 A:HIS267 4.9 27.6 1.0
CH2 D:TRP221 4.9 35.7 1.0
NE2 A:HIS267 5.0 28.8 1.0

Reference:

C.P.Mpamhanga, D.Spinks, L.B.Tulloch, E.J.Shanks, D.A.Robinson, I.T.Collie, A.H.Fairlamb, P.G.Wyatt, J.A.Frearson, W.N.Hunter, I.H.Gilbert, R.Brenk. One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived From Fragment Hits Discovered By Virtual Screening. J.Med.Chem. V. 52 4454 2009.
ISSN: ISSN 0022-2623
PubMed: 19527033
DOI: 10.1021/JM900414X
Page generated: Sat Jul 20 12:42:48 2024

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