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: Tue Aug 6 10:00:09 2024
|