Atomistry » Chlorine » PDB 4kbb-4kmx » 4kbn
Atomistry »
  Chlorine »
    PDB 4kbb-4kmx »
      4kbn »

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

Go back to Chlorine Binding Sites List in 4kbn
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

Go back to Chlorine Binding Sites List in 4kbn
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

Go back to Chlorine Binding Sites List in 4kbn
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

Go back to Chlorine Binding Sites List in 4kbn
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

Go back to Chlorine Binding Sites List in 4kbn
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

Go back to Chlorine Binding Sites List in 4kbn
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

Go back to Chlorine Binding Sites List in 4kbn
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

Go back to Chlorine Binding Sites List in 4kbn
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: Sun Jul 21 18:06:36 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy