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Iron in PDB 5urc: Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease

Protein crystallography data

The structure of Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease, PDB code: 5urc was solved by P.P.Pagare, R.S.Safo, A.Gazi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.32 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.642, 83.328, 104.954, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.3

Iron Binding Sites:

The binding sites of Iron atom in the Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease (pdb code 5urc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease, PDB code: 5urc:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5urc

Go back to Iron Binding Sites List in 5urc
Iron binding site 1 out of 4 in the Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:19.0
occ:1.00
FE A:HEM202 0.0 19.0 1.0
C A:CMO201 1.9 17.4 1.0
ND A:HEM202 2.0 18.0 1.0
NB A:HEM202 2.0 16.3 1.0
NA A:HEM202 2.0 17.1 1.0
NC A:HEM202 2.0 17.2 1.0
NE2 A:HIS87 2.0 16.8 1.0
CE1 A:HIS87 3.0 15.9 1.0
C4D A:HEM202 3.0 19.6 1.0
C1C A:HEM202 3.1 17.1 1.0
C1A A:HEM202 3.1 18.8 1.0
C4B A:HEM202 3.1 16.6 1.0
C1D A:HEM202 3.1 18.3 1.0
C1B A:HEM202 3.1 16.9 1.0
C4A A:HEM202 3.1 17.9 1.0
C4C A:HEM202 3.1 17.9 1.0
CD2 A:HIS87 3.1 16.8 1.0
O A:CMO201 3.1 21.8 1.0
CHC A:HEM202 3.4 16.5 1.0
CHA A:HEM202 3.4 20.6 1.0
CHD A:HEM202 3.5 17.2 1.0
CHB A:HEM202 3.5 15.2 1.0
ND1 A:HIS87 4.2 16.5 1.0
CG A:HIS87 4.2 15.5 1.0
C3D A:HEM202 4.3 19.4 1.0
C2A A:HEM202 4.3 19.1 1.0
C2D A:HEM202 4.3 20.4 1.0
C2C A:HEM202 4.3 16.4 1.0
C2B A:HEM202 4.3 16.9 1.0
C3A A:HEM202 4.3 17.9 1.0
C3B A:HEM202 4.3 17.1 1.0
C3C A:HEM202 4.3 17.4 1.0
CE1 A:HIS58 4.5 23.2 1.0
NE2 A:HIS58 4.9 23.6 1.0
CG2 A:VAL62 4.9 17.8 1.0

Iron binding site 2 out of 4 in 5urc

Go back to Iron Binding Sites List in 5urc
Iron binding site 2 out of 4 in the Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:22.8
occ:1.00
FE B:HEM202 0.0 22.8 1.0
C B:CMO201 1.9 24.1 1.0
NC B:HEM202 2.0 24.2 1.0
NB B:HEM202 2.0 22.3 1.0
NA B:HEM202 2.0 23.2 1.0
ND B:HEM202 2.0 25.3 1.0
NE2 B:HIS92 2.0 21.6 1.0
CE1 B:HIS92 3.0 22.6 1.0
CD2 B:HIS92 3.1 22.1 1.0
C1C B:HEM202 3.1 22.6 1.0
C1D B:HEM202 3.1 25.6 1.0
C4C B:HEM202 3.1 25.2 1.0
C1A B:HEM202 3.1 23.3 1.0
C1B B:HEM202 3.1 20.4 1.0
C4B B:HEM202 3.1 20.9 1.0
C4A B:HEM202 3.1 21.7 1.0
C4D B:HEM202 3.1 25.1 1.0
O B:CMO201 3.1 26.4 1.0
CHC B:HEM202 3.4 21.6 1.0
CHD B:HEM202 3.4 25.9 1.0
CHA B:HEM202 3.4 23.1 1.0
CHB B:HEM202 3.5 20.4 1.0
ND1 B:HIS92 4.2 21.6 1.0
CG B:HIS92 4.2 21.5 1.0
C2A B:HEM202 4.3 21.7 1.0
C2C B:HEM202 4.3 24.2 1.0
C3A B:HEM202 4.3 21.2 1.0
C2D B:HEM202 4.3 27.1 1.0
C3C B:HEM202 4.3 24.4 1.0
C3D B:HEM202 4.3 26.9 1.0
C2B B:HEM202 4.3 19.1 1.0
C3B B:HEM202 4.3 22.4 1.0
CE1 B:HIS63 4.4 23.5 1.0
CG2 B:VAL67 4.9 15.5 1.0

Iron binding site 3 out of 4 in 5urc

Go back to Iron Binding Sites List in 5urc
Iron binding site 3 out of 4 in the Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:17.6
occ:1.00
FE C:HEM202 0.0 17.6 1.0
C C:CMO201 1.9 16.5 1.0
ND C:HEM202 2.0 16.9 1.0
NA C:HEM202 2.0 17.4 1.0
NE2 C:HIS87 2.0 15.7 1.0
NC C:HEM202 2.0 16.1 1.0
NB C:HEM202 2.0 17.0 1.0
CE1 C:HIS87 3.0 17.2 1.0
C4D C:HEM202 3.0 18.9 1.0
C1D C:HEM202 3.0 17.5 1.0
C1A C:HEM202 3.0 19.9 1.0
CD2 C:HIS87 3.1 18.4 1.0
C1B C:HEM202 3.1 18.0 1.0
C4A C:HEM202 3.1 19.0 1.0
C4C C:HEM202 3.1 17.2 1.0
C1C C:HEM202 3.1 16.2 1.0
C4B C:HEM202 3.1 17.0 1.0
O C:CMO201 3.1 20.4 1.0
CHA C:HEM202 3.4 18.9 1.0
CHD C:HEM202 3.4 18.1 1.0
CHB C:HEM202 3.5 15.5 1.0
CHC C:HEM202 3.5 16.2 1.0
ND1 C:HIS87 4.2 15.7 1.0
CG C:HIS87 4.2 15.3 1.0
C3D C:HEM202 4.2 17.8 1.0
C2D C:HEM202 4.3 17.5 1.0
C2A C:HEM202 4.3 19.3 1.0
C3A C:HEM202 4.3 18.1 1.0
C2B C:HEM202 4.3 17.5 1.0
C2C C:HEM202 4.3 17.2 1.0
C3B C:HEM202 4.3 16.7 1.0
C3C C:HEM202 4.3 17.2 1.0
NE2 C:HIS58 4.6 20.4 1.0
CG2 C:VAL62 4.9 20.3 1.0

Iron binding site 4 out of 4 in 5urc

Go back to Iron Binding Sites List in 5urc
Iron binding site 4 out of 4 in the Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:20.7
occ:1.00
FE D:HEM202 0.0 20.7 1.0
C D:CMO201 1.9 20.7 1.0
ND D:HEM202 2.0 19.7 1.0
NC D:HEM202 2.0 20.6 1.0
NA D:HEM202 2.0 18.9 1.0
NE2 D:HIS92 2.0 19.2 1.0
NB D:HEM202 2.0 18.4 1.0
CE1 D:HIS92 3.0 19.4 1.0
C4D D:HEM202 3.0 20.0 1.0
C1D D:HEM202 3.0 20.8 1.0
C1C D:HEM202 3.1 19.0 1.0
C4A D:HEM202 3.1 18.5 1.0
C1A D:HEM202 3.1 20.1 1.0
C4B D:HEM202 3.1 19.5 1.0
C1B D:HEM202 3.1 19.8 1.0
C4C D:HEM202 3.1 19.0 1.0
CD2 D:HIS92 3.1 20.2 1.0
O D:CMO201 3.1 23.6 1.0
CHC D:HEM202 3.4 18.1 1.0
CHA D:HEM202 3.4 20.0 1.0
CHD D:HEM202 3.4 19.0 1.0
CHB D:HEM202 3.4 19.0 1.0
ND1 D:HIS92 4.2 18.2 1.0
CG D:HIS92 4.2 18.9 1.0
C3D D:HEM202 4.3 20.8 1.0
C2D D:HEM202 4.3 20.9 1.0
C2A D:HEM202 4.3 19.9 1.0
C2C D:HEM202 4.3 18.7 1.0
C3A D:HEM202 4.3 20.4 1.0
C3C D:HEM202 4.3 17.8 1.0
C2B D:HEM202 4.3 21.0 1.0
C3B D:HEM202 4.3 21.8 1.0
CE1 D:HIS63 4.4 17.5 1.0
CG2 D:VAL67 4.8 22.2 1.0

Reference:

G.G.Xu, P.P.Pagare, M.S.Ghatge, R.P.Safo, A.Gazi, Q.Chen, T.David, A.B.Alabbas, F.N.Musayev, J.Venitz, Y.Zhang, M.K.Safo, O.Abdulmalik. Design, Synthesis, and Biological Evaluation of Ester and Ether Derivatives of Antisickling Agent 5-Hmf For the Treatment of Sickle Cell Disease. Mol. Pharm. V. 14 3499 2017.
ISSN: ESSN 1543-8392
PubMed: 28858508
DOI: 10.1021/ACS.MOLPHARMACEUT.7B00553
Page generated: Wed Aug 6 01:57:37 2025

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