Iron in PDB 7jy3: Structure of Hba with Compound 23 (Pf-07059013)
Protein crystallography data
The structure of Structure of Hba with Compound 23 (Pf-07059013), PDB code: 7jy3
was solved by
J.Jasti,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.69 /
1.48
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.77,
82.47,
65.08,
90,
99.54,
90
|
R / Rfree (%)
|
18 /
20.7
|
Other elements in 7jy3:
The structure of Structure of Hba with Compound 23 (Pf-07059013) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Hba with Compound 23 (Pf-07059013)
(pdb code 7jy3). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of Hba with Compound 23 (Pf-07059013), PDB code: 7jy3:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7jy3
Go back to
Iron Binding Sites List in 7jy3
Iron binding site 1 out
of 4 in the Structure of Hba with Compound 23 (Pf-07059013)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Hba with Compound 23 (Pf-07059013) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:17.6
occ:1.00
|
FE
|
A:HEM201
|
0.0
|
17.6
|
1.0
|
NC
|
A:HEM201
|
1.9
|
17.4
|
1.0
|
NB
|
A:HEM201
|
2.0
|
17.3
|
1.0
|
NA
|
A:HEM201
|
2.0
|
18.1
|
1.0
|
ND
|
A:HEM201
|
2.0
|
17.7
|
1.0
|
O1
|
A:OXY202
|
2.0
|
32.2
|
1.0
|
NE2
|
A:HIS87
|
2.1
|
15.6
|
1.0
|
O2
|
A:OXY202
|
2.8
|
37.4
|
1.0
|
C4B
|
A:HEM201
|
2.9
|
17.5
|
1.0
|
C1C
|
A:HEM201
|
3.0
|
17.2
|
1.0
|
C1B
|
A:HEM201
|
3.0
|
17.7
|
1.0
|
C4D
|
A:HEM201
|
3.0
|
18.1
|
1.0
|
C1D
|
A:HEM201
|
3.0
|
18.0
|
1.0
|
C4A
|
A:HEM201
|
3.0
|
18.1
|
1.0
|
CE1
|
A:HIS87
|
3.0
|
15.8
|
1.0
|
C4C
|
A:HEM201
|
3.0
|
17.6
|
1.0
|
C1A
|
A:HEM201
|
3.0
|
18.4
|
1.0
|
CD2
|
A:HIS87
|
3.2
|
15.1
|
1.0
|
CHC
|
A:HEM201
|
3.3
|
18.0
|
1.0
|
CHB
|
A:HEM201
|
3.4
|
18.3
|
1.0
|
CHA
|
A:HEM201
|
3.4
|
18.7
|
1.0
|
CHD
|
A:HEM201
|
3.4
|
18.3
|
1.0
|
C2C
|
A:HEM201
|
4.2
|
17.8
|
1.0
|
ND1
|
A:HIS87
|
4.2
|
16.5
|
1.0
|
C2B
|
A:HEM201
|
4.2
|
17.8
|
1.0
|
C3B
|
A:HEM201
|
4.2
|
18.0
|
1.0
|
C3C
|
A:HEM201
|
4.3
|
17.8
|
1.0
|
CG
|
A:HIS87
|
4.3
|
14.6
|
1.0
|
NE2
|
A:HIS58
|
4.3
|
27.9
|
1.0
|
C3A
|
A:HEM201
|
4.3
|
18.8
|
1.0
|
C2D
|
A:HEM201
|
4.3
|
18.4
|
1.0
|
C3D
|
A:HEM201
|
4.3
|
18.6
|
1.0
|
C2A
|
A:HEM201
|
4.3
|
19.0
|
1.0
|
CE1
|
A:HIS58
|
4.6
|
27.6
|
1.0
|
CG2
|
A:VAL62
|
4.9
|
23.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 7jy3
Go back to
Iron Binding Sites List in 7jy3
Iron binding site 2 out
of 4 in the Structure of Hba with Compound 23 (Pf-07059013)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Hba with Compound 23 (Pf-07059013) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:16.3
occ:1.00
|
FE
|
B:HEM201
|
0.0
|
16.3
|
1.0
|
NA
|
B:HEM201
|
2.0
|
16.7
|
1.0
|
ND
|
B:HEM201
|
2.0
|
16.7
|
1.0
|
NC
|
B:HEM201
|
2.0
|
16.2
|
1.0
|
NB
|
B:HEM201
|
2.0
|
16.1
|
1.0
|
O1
|
B:OXY202
|
2.0
|
27.7
|
1.0
|
NE2
|
B:HIS92
|
2.1
|
16.7
|
1.0
|
O2
|
B:OXY202
|
2.8
|
35.5
|
1.0
|
C4D
|
B:HEM201
|
3.0
|
17.1
|
1.0
|
C1B
|
B:HEM201
|
3.0
|
16.6
|
1.0
|
C1A
|
B:HEM201
|
3.0
|
17.0
|
1.0
|
C4A
|
B:HEM201
|
3.0
|
16.8
|
1.0
|
C1D
|
B:HEM201
|
3.0
|
17.1
|
1.0
|
C4C
|
B:HEM201
|
3.0
|
16.5
|
1.0
|
C4B
|
B:HEM201
|
3.0
|
16.4
|
1.0
|
CE1
|
B:HIS92
|
3.0
|
16.5
|
1.0
|
C1C
|
B:HEM201
|
3.1
|
16.1
|
1.0
|
CD2
|
B:HIS92
|
3.1
|
17.3
|
1.0
|
CHB
|
B:HEM201
|
3.4
|
17.0
|
1.0
|
CHA
|
B:HEM201
|
3.4
|
17.5
|
1.0
|
CHD
|
B:HEM201
|
3.4
|
17.3
|
1.0
|
CHC
|
B:HEM201
|
3.4
|
16.8
|
1.0
|
NE2
|
B:HIS63
|
4.2
|
24.9
|
1.0
|
ND1
|
B:HIS92
|
4.2
|
18.4
|
1.0
|
C2A
|
B:HEM201
|
4.2
|
17.5
|
1.0
|
C3A
|
B:HEM201
|
4.2
|
17.4
|
1.0
|
CG
|
B:HIS92
|
4.2
|
17.6
|
1.0
|
C2B
|
B:HEM201
|
4.3
|
16.7
|
1.0
|
C2D
|
B:HEM201
|
4.3
|
17.6
|
1.0
|
C2C
|
B:HEM201
|
4.3
|
16.7
|
1.0
|
C3D
|
B:HEM201
|
4.3
|
17.9
|
1.0
|
C3C
|
B:HEM201
|
4.3
|
16.7
|
1.0
|
C3B
|
B:HEM201
|
4.3
|
16.8
|
1.0
|
CG2
|
B:VAL67
|
4.7
|
18.9
|
1.0
|
CE1
|
B:HIS63
|
4.9
|
24.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 7jy3
Go back to
Iron Binding Sites List in 7jy3
Iron binding site 3 out
of 4 in the Structure of Hba with Compound 23 (Pf-07059013)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Hba with Compound 23 (Pf-07059013) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe202
b:14.9
occ:1.00
|
FE
|
C:HEM202
|
0.0
|
14.9
|
1.0
|
NC
|
C:HEM202
|
2.0
|
14.7
|
1.0
|
NA
|
C:HEM202
|
2.0
|
15.3
|
1.0
|
ND
|
C:HEM202
|
2.0
|
14.9
|
1.0
|
O1
|
C:OXY203
|
2.0
|
24.5
|
1.0
|
NB
|
C:HEM202
|
2.0
|
14.6
|
1.0
|
NE2
|
C:HIS87
|
2.1
|
14.9
|
1.0
|
O2
|
C:OXY203
|
2.7
|
27.6
|
1.0
|
C4D
|
C:HEM202
|
3.0
|
15.3
|
1.0
|
C4B
|
C:HEM202
|
3.0
|
14.8
|
1.0
|
C1C
|
C:HEM202
|
3.0
|
14.6
|
1.0
|
C1D
|
C:HEM202
|
3.0
|
15.2
|
1.0
|
C1B
|
C:HEM202
|
3.0
|
15.0
|
1.0
|
C1A
|
C:HEM202
|
3.0
|
15.5
|
1.0
|
C4A
|
C:HEM202
|
3.0
|
15.3
|
1.0
|
C4C
|
C:HEM202
|
3.0
|
14.8
|
1.0
|
CE1
|
C:HIS87
|
3.0
|
15.2
|
1.0
|
CD2
|
C:HIS87
|
3.2
|
15.2
|
1.0
|
CHC
|
C:HEM202
|
3.4
|
15.3
|
1.0
|
CHA
|
C:HEM202
|
3.4
|
15.9
|
1.0
|
CHB
|
C:HEM202
|
3.4
|
15.5
|
1.0
|
CHD
|
C:HEM202
|
3.4
|
15.5
|
1.0
|
ND1
|
C:HIS87
|
4.2
|
15.7
|
1.0
|
C2C
|
C:HEM202
|
4.2
|
15.0
|
1.0
|
C2B
|
C:HEM202
|
4.2
|
15.0
|
1.0
|
C2D
|
C:HEM202
|
4.3
|
15.6
|
1.0
|
C3C
|
C:HEM202
|
4.3
|
15.1
|
1.0
|
C3B
|
C:HEM202
|
4.3
|
15.2
|
1.0
|
C3D
|
C:HEM202
|
4.3
|
15.8
|
1.0
|
NE2
|
C:HIS58
|
4.3
|
19.5
|
1.0
|
C3A
|
C:HEM202
|
4.3
|
16.0
|
1.0
|
CG
|
C:HIS87
|
4.3
|
14.1
|
1.0
|
C2A
|
C:HEM202
|
4.3
|
16.1
|
1.0
|
CE1
|
C:HIS58
|
4.6
|
20.0
|
1.0
|
CG2
|
C:VAL62
|
4.9
|
17.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 7jy3
Go back to
Iron Binding Sites List in 7jy3
Iron binding site 4 out
of 4 in the Structure of Hba with Compound 23 (Pf-07059013)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Hba with Compound 23 (Pf-07059013) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:14.6
occ:1.00
|
FE
|
D:HEM201
|
0.0
|
14.6
|
1.0
|
NA
|
D:HEM201
|
2.0
|
14.9
|
1.0
|
ND
|
D:HEM201
|
2.0
|
14.8
|
1.0
|
NB
|
D:HEM201
|
2.0
|
14.3
|
1.0
|
O1
|
D:OXY202
|
2.0
|
21.7
|
1.0
|
NC
|
D:HEM201
|
2.0
|
14.4
|
1.0
|
NE2
|
D:HIS92
|
2.1
|
15.7
|
1.0
|
O2
|
D:OXY202
|
2.8
|
30.6
|
1.0
|
C4D
|
D:HEM201
|
3.0
|
15.3
|
1.0
|
C1B
|
D:HEM201
|
3.0
|
14.7
|
1.0
|
C1D
|
D:HEM201
|
3.0
|
15.2
|
1.0
|
C4C
|
D:HEM201
|
3.0
|
14.7
|
1.0
|
C4B
|
D:HEM201
|
3.0
|
14.5
|
1.0
|
C1A
|
D:HEM201
|
3.0
|
15.2
|
1.0
|
C4A
|
D:HEM201
|
3.0
|
14.9
|
1.0
|
CE1
|
D:HIS92
|
3.1
|
14.8
|
1.0
|
C1C
|
D:HEM201
|
3.1
|
14.3
|
1.0
|
CD2
|
D:HIS92
|
3.2
|
15.9
|
1.0
|
CHA
|
D:HEM201
|
3.4
|
15.6
|
1.0
|
CHB
|
D:HEM201
|
3.4
|
15.2
|
1.0
|
CHD
|
D:HEM201
|
3.4
|
15.5
|
1.0
|
CHC
|
D:HEM201
|
3.4
|
14.9
|
1.0
|
NE2
|
D:HIS63
|
4.2
|
20.8
|
1.0
|
ND1
|
D:HIS92
|
4.2
|
15.9
|
1.0
|
C2B
|
D:HEM201
|
4.2
|
14.8
|
1.0
|
CG
|
D:HIS92
|
4.3
|
16.4
|
1.0
|
C2D
|
D:HEM201
|
4.3
|
15.7
|
1.0
|
C2A
|
D:HEM201
|
4.3
|
15.7
|
1.0
|
C2C
|
D:HEM201
|
4.3
|
14.8
|
1.0
|
C3A
|
D:HEM201
|
4.3
|
15.5
|
1.0
|
C3C
|
D:HEM201
|
4.3
|
14.9
|
1.0
|
C3D
|
D:HEM201
|
4.3
|
16.0
|
1.0
|
C3B
|
D:HEM201
|
4.3
|
15.0
|
1.0
|
CG2
|
D:VAL67
|
4.7
|
14.7
|
1.0
|
CE1
|
D:HIS63
|
4.9
|
20.8
|
1.0
|
|
Reference:
A.Gopalsamy,
A.E.Aulabaugh,
A.Barakat,
K.C.Beaumont,
S.Cabral,
D.P.Canterbury,
A.Casimiro-Garcia,
J.S.Chang,
M.Z.Chen,
C.Choi,
R.L.Dow,
O.O.Fadeyi,
X.Feng,
S.P.France,
R.M.Howard,
J.M.Janz,
J.Jasti,
R.Jasuja,
L.H.Jones,
A.King-Ahmad,
K.M.Knee,
J.T.Kohrt,
C.Limberakis,
S.Liras,
C.A.Martinez,
K.F.Mcclure,
A.Narayanan,
J.Narula,
J.J.Novak,
T.N.O'connell,
M.D.Parikh,
D.W.Piotrowski,
O.Plotnikova,
R.P.Robinson,
P.V.Sahasrabudhe,
R.Sharma,
B.A.Thuma,
D.Vasa,
L.Wei,
A.Z.Wenzel,
J.M.Withka,
J.Xiao,
H.G.Yayla.
Pf-07059013: A Noncovalent Modulator of Hemoglobin For Treatment of Sickle Cell Disease. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33356244
DOI: 10.1021/ACS.JMEDCHEM.0C01518
Page generated: Thu Aug 8 05:56:48 2024
|