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Chlorine in PDB 4kbn: Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE

Enzymatic activity of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE

All present enzymatic activity of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE:
1.5.1.3;

Protein crystallography data

The structure of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE, PDB code: 4kbn was solved by K.M.Lamb, A.C.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 1.84
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 87.669, 93.784, 95.991, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 27.7

Other elements in 4kbn:

The structure of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE also contains other interesting chemical elements:

Strontium (Sr) 1 atom
Magnesium (Mg) 9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE (pdb code 4kbn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE, PDB code: 4kbn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4kbn

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Chlorine binding site 1 out of 8 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:44.8
occ:1.00
 O A:HOH464 3.0 30.3 1.0
O A:VAL169 4.4 20.3 1.0
MG A:MG209 4.6 29.8 1.0
CB A:ASP168 4.8 19.8 1.0
OD2 A:ASP168 4.9 18.9 1.0

Chlorine binding site 2 out of 8 in 4kbn

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Chlorine binding site 2 out of 8 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:43.8
occ:1.00
 N A:GLY174 2.9 21.9 1.0
CG A:GLU171 3.5 29.4 1.0
N A:LYS173 3.5 25.9 0.6
N A:LYS173 3.5 26.0 0.4
CA A:GLY174 3.6 29.0 1.0
O B:GLY2 3.7 42.4 1.0
O A:HOH363 3.7 39.7 1.0
CB B:HIS130 3.8 25.5 1.0
CD A:GLU171 3.9 36.2 1.0
C A:LYS173 3.9 22.6 0.6
C A:LYS173 3.9 22.6 0.4
CB B:SER3 3.9 40.0 1.0
C A:GLU172 4.0 21.2 1.0
CA A:LYS173 4.0 26.6 0.6
CA A:LYS173 4.1 26.6 0.4
O B:HOH372 4.2 43.6 1.0
CG B:HIS130 4.2 27.6 1.0
CA A:GLU172 4.2 25.8 1.0
ND1 B:HIS130 4.2 27.8 1.0
C B:GLY2 4.2 47.9 1.0
O A:GLU171 4.3 26.9 1.0
OE2 A:GLU171 4.3 43.7 1.0
C A:GLU171 4.3 19.3 1.0
N A:GLU172 4.3 22.8 1.0
OE1 A:GLU171 4.3 39.6 1.0
CB A:GLU171 4.4 30.6 1.0
O A:HOH439 4.5 39.1 1.0
C A:GLY174 4.6 31.9 1.0
O A:GLU172 4.7 24.2 1.0
SR B:SR201 4.7 86.7 0.1
CA B:SER3 4.7 32.9 1.0
N B:SER3 4.7 43.1 1.0
OG B:SER3 4.7 41.6 1.0
N A:ILE175 4.8 26.8 1.0
CA B:GLY2 5.0 55.8 1.0

Chlorine binding site 3 out of 8 in 4kbn

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Chlorine binding site 3 out of 8 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:63.0
occ:1.00
 OG A:SER42 2.7 39.3 1.0
O A:HOH469 2.8 35.5 1.0
CG2 A:VAL43 3.3 43.0 1.0
CB A:SER42 3.5 39.8 1.0
O A:SER42 3.6 41.3 1.0
C A:SER42 3.9 44.9 1.0
N A:VAL43 4.3 42.3 1.0
CA A:SER42 4.3 37.0 1.0
CB A:VAL43 4.6 37.3 1.0
CA A:VAL43 4.7 38.7 1.0
OD2 A:ASP110 5.0 34.8 1.0

Chlorine binding site 4 out of 8 in 4kbn

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Chlorine binding site 4 out of 8 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:72.7
occ:1.00
 NH1 A:ARG70 2.8 22.7 1.0
NH2 A:ARG70 2.8 26.9 1.0
NE2 A:GLN35 3.1 40.2 1.0
CZ A:ARG70 3.2 28.9 1.0
CG A:GLN35 3.3 39.2 1.0
CD A:GLN35 3.6 48.5 1.0
CZ A:PHE31 3.9 32.2 1.0
CE2 A:PHE34 4.2 36.0 1.0
CB A:GLN35 4.2 24.5 1.0
CA A:GLN35 4.3 22.5 1.0
CD2 A:PHE34 4.4 29.6 1.0
CE1 A:PHE31 4.4 36.8 1.0
CD2 A:LEU67 4.4 34.0 1.0
NE A:ARG70 4.5 25.9 1.0
CAK A:25U201 4.5 39.3 1.0
CE2 A:PHE31 4.6 35.9 1.0
O A:HOH480 4.7 32.5 1.0
OE1 A:GLN35 4.7 48.2 1.0
NAP A:25U201 4.7 49.0 1.0
CD1 A:LEU67 4.8 25.6 1.0
CB A:LEU67 4.8 27.4 1.0
CG A:LEU67 4.9 29.0 1.0
N A:GLN35 5.0 18.7 1.0

Chlorine binding site 5 out of 8 in 4kbn

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Chlorine binding site 5 out of 8 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:56.6
occ:1.00
 O A:HOH318 2.7 23.3 1.0
OD1 A:ASN29 3.4 36.1 1.0
CD A:ARG32 3.4 32.1 0.5
CD A:ARG32 3.6 31.8 0.5
NH1 A:ARG32 3.8 49.9 0.5
CB A:ARG32 3.8 19.1 0.5
CG A:ASN29 3.8 36.0 1.0
CB A:ARG32 3.8 19.0 0.5
O A:HOH383 4.0 31.6 1.0
CB A:ASN29 4.0 24.2 1.0
CA A:ASN29 4.2 24.4 1.0
CG A:ARG32 4.2 31.2 0.5
CG A:ARG32 4.3 31.1 0.5
O A:HOH316 4.3 28.8 1.0
O A:HOH382 4.4 34.6 1.0
O A:ASN29 4.5 20.1 1.0
NE A:ARG32 4.5 41.0 0.5
NE A:ARG32 4.5 34.0 0.5
CZ A:ARG32 4.6 51.1 0.5
ND2 A:ASN29 4.8 33.6 1.0
NH1 A:ARG32 4.8 50.7 0.5
C A:ASN29 4.9 24.8 1.0

Chlorine binding site 6 out of 8 in 4kbn

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Chlorine binding site 6 out of 8 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl205

b:61.9
occ:1.00
 O B:HOH308 2.6 30.9 1.0
ND2 B:ASN5 3.2 29.2 1.0
OG B:SER3 3.5 41.6 1.0
O B:HOH377 3.5 41.3 1.0
SR B:SR201 3.5 86.7 0.1
CB B:SER3 3.7 40.0 1.0
CE B:MET111 3.8 29.4 0.5
CA A:GLY174 4.0 29.0 1.0
O A:GLY174 4.0 27.6 1.0
CG B:ASN5 4.1 24.9 1.0
OD1 B:ASN5 4.1 24.5 1.0
CG B:MET111 4.2 31.6 0.5
SD B:MET111 4.2 40.6 0.5
O B:SER3 4.2 35.0 1.0
CG2 B:VAL1 4.3 46.7 1.0
CB B:MET111 4.3 25.0 0.5
C B:SER3 4.3 34.0 1.0
CB B:MET111 4.4 25.0 0.5
C A:GLY174 4.4 31.9 1.0
CG B:MET111 4.6 31.3 0.5
CA B:SER3 4.6 32.9 1.0
CA B:MET111 4.7 23.1 0.5
CG1 B:VAL1 4.7 52.7 1.0
CA B:MET111 4.7 23.1 0.5
N B:LEU4 4.8 32.9 1.0

Chlorine binding site 7 out of 8 in 4kbn

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Chlorine binding site 7 out of 8 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl207

b:64.7
occ:1.00
 N B:PRO163 3.4 33.1 1.0
CG B:PRO163 3.6 35.9 1.0
CD B:PRO163 3.6 29.8 1.0
CA B:PRO163 3.7 31.2 1.0
O A:HOH474 3.7 52.5 1.0
C B:TYR162 3.8 32.9 1.0
CG B:GLU161 3.9 49.4 1.0
CB B:PRO163 4.1 38.1 1.0
O B:TYR162 4.3 29.8 1.0
CA B:TYR162 4.3 31.0 1.0
N B:TYR162 4.5 31.0 1.0
O A:HOH468 4.5 37.9 1.0
OE2 B:GLU161 4.7 68.9 1.0
CD B:GLU161 4.8 71.2 1.0
CB B:GLU161 5.0 39.8 1.0

Chlorine binding site 8 out of 8 in 4kbn

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Chlorine binding site 8 out of 8 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl208

b:81.3
occ:1.00
 O B:HOH366 2.6 46.0 1.0
O B:HOH346 2.9 31.4 1.0
CB B:GLN35 3.5 25.4 1.0
O B:HOH449 3.6 36.9 1.0
CG B:GLN35 3.7 39.0 1.0
CG B:ARG32 4.2 28.2 1.0
NE2 B:GLN35 4.2 39.8 1.0
CA B:ARG32 4.4 19.1 1.0
CD B:GLN35 4.5 50.0 1.0
CB B:ARG32 4.6 24.4 1.0
O B:ARG32 4.7 21.7 1.0
CA B:GLN35 4.9 24.7 1.0
O B:HOH411 5.0 39.8 1.0

Reference:

K.M.Lamb, N.G-Dayanandan, D.L.Wright, A.C.Anderson. Elucidating Features That Drive the Design of Selective Antifolates Using Crystal Structures of Human Dihydrofolate Reductase. Biochemistry V. 52 7318 2013.
ISSN: ISSN 0006-2960
PubMed: 24053334
DOI: 10.1021/BI400852H
Page generated: Fri Jul 11 17:44:05 2025

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