Cadmium in PDB 7up3: NDM1-Inhibitor Co-Structure
Protein crystallography data
The structure of NDM1-Inhibitor Co-Structure, PDB code: 7up3
was solved by
G.Scapin,
T.O.Fischmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.72 /
1.40
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
69.564,
73.913,
77.325,
90,
90,
90
|
R / Rfree (%)
|
18 /
19
|
Other elements in 7up3:
The structure of NDM1-Inhibitor Co-Structure also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the NDM1-Inhibitor Co-Structure
(pdb code 7up3). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the
NDM1-Inhibitor Co-Structure, PDB code: 7up3:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
Cadmium binding site 1 out
of 6 in 7up3
Go back to
Cadmium Binding Sites List in 7up3
Cadmium binding site 1 out
of 6 in the NDM1-Inhibitor Co-Structure
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd301
b:19.6
occ:1.00
|
OE2
|
A:GLU152
|
2.3
|
20.2
|
1.0
|
O
|
A:HOH513
|
2.3
|
28.6
|
1.0
|
OE2
|
B:GLU227
|
2.3
|
25.8
|
1.0
|
OD2
|
A:ASP223
|
2.3
|
17.6
|
1.0
|
OE1
|
B:GLU227
|
2.4
|
23.5
|
1.0
|
OE1
|
A:GLU152
|
2.5
|
20.2
|
1.0
|
CD
|
A:GLU152
|
2.7
|
21.5
|
1.0
|
CD
|
B:GLU227
|
2.7
|
23.5
|
1.0
|
CG
|
A:ASP223
|
3.0
|
21.5
|
1.0
|
OD1
|
A:ASP223
|
3.0
|
23.0
|
1.0
|
NE2
|
A:HIS122
|
4.2
|
16.4
|
1.0
|
CG
|
A:GLU152
|
4.2
|
16.8
|
1.0
|
CG
|
B:GLU227
|
4.2
|
19.9
|
1.0
|
O
|
A:HOH477
|
4.3
|
17.9
|
1.0
|
NE2
|
B:HIS228
|
4.3
|
16.3
|
1.0
|
O
|
A:HOH487
|
4.4
|
36.5
|
1.0
|
CB
|
A:ASP223
|
4.5
|
18.6
|
1.0
|
CE1
|
B:HIS228
|
4.5
|
16.3
|
1.0
|
O
|
A:HOH438
|
4.6
|
23.8
|
1.0
|
CD2
|
A:HIS122
|
4.7
|
16.0
|
1.0
|
O
|
B:HOH513
|
4.9
|
22.6
|
1.0
|
|
Cadmium binding site 2 out
of 6 in 7up3
Go back to
Cadmium Binding Sites List in 7up3
Cadmium binding site 2 out
of 6 in the NDM1-Inhibitor Co-Structure
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd302
b:18.0
occ:0.70
|
OD2
|
A:ASP130
|
2.2
|
22.7
|
1.0
|
OD2
|
A:ASP95
|
2.3
|
23.6
|
1.0
|
O
|
A:HOH496
|
2.3
|
17.1
|
1.0
|
CG
|
A:ASP130
|
3.2
|
19.6
|
1.0
|
CG
|
A:ASP95
|
3.2
|
21.6
|
1.0
|
OD1
|
A:ASP95
|
3.4
|
20.0
|
1.0
|
CB
|
A:ASP130
|
3.6
|
16.8
|
1.0
|
O
|
A:GLY127
|
4.1
|
16.2
|
1.0
|
OD1
|
A:ASP130
|
4.2
|
20.8
|
1.0
|
O
|
A:HOH486
|
4.3
|
21.2
|
1.0
|
O
|
A:HOH488
|
4.3
|
24.8
|
1.0
|
O
|
A:HOH451
|
4.5
|
15.6
|
1.0
|
N
|
A:ASP130
|
4.5
|
15.3
|
1.0
|
CB
|
A:ASP95
|
4.6
|
17.3
|
1.0
|
CA
|
A:ASP130
|
4.7
|
16.2
|
1.0
|
CG2
|
A:VAL155
|
4.7
|
20.0
|
1.0
|
|
Cadmium binding site 3 out
of 6 in 7up3
Go back to
Cadmium Binding Sites List in 7up3
Cadmium binding site 3 out
of 6 in the NDM1-Inhibitor Co-Structure
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd304
b:17.9
occ:1.00
|
OD2
|
A:ASP124
|
2.2
|
17.4
|
1.0
|
N3
|
A:NZ0305
|
2.2
|
20.9
|
1.0
|
NE2
|
A:HIS250
|
2.3
|
16.8
|
1.0
|
N4
|
A:NZ0305
|
2.5
|
16.8
|
1.0
|
SG
|
A:CYS208
|
2.5
|
17.7
|
1.0
|
N2
|
A:NZ0305
|
3.2
|
23.9
|
1.0
|
CG
|
A:ASP124
|
3.2
|
17.3
|
1.0
|
C5
|
A:NZ0305
|
3.3
|
21.4
|
1.0
|
CE1
|
A:HIS250
|
3.3
|
16.7
|
1.0
|
CD2
|
A:HIS250
|
3.3
|
17.5
|
1.0
|
C4
|
A:NZ0305
|
3.5
|
24.5
|
1.0
|
S
|
A:NZ0305
|
3.5
|
19.8
|
1.0
|
CB
|
A:CYS208
|
3.6
|
15.9
|
1.0
|
OD1
|
A:ASP124
|
3.6
|
18.3
|
1.0
|
C6
|
A:NZ0305
|
3.6
|
22.6
|
1.0
|
ZN
|
A:ZN303
|
3.7
|
15.8
|
1.0
|
O
|
A:NZ0305
|
4.1
|
20.3
|
1.0
|
N1
|
A:NZ0305
|
4.3
|
23.5
|
1.0
|
NE2
|
A:HIS189
|
4.3
|
13.8
|
1.0
|
N
|
A:NZ0305
|
4.4
|
22.8
|
1.0
|
CG
|
A:HIS250
|
4.4
|
18.8
|
1.0
|
ND1
|
A:HIS250
|
4.4
|
19.1
|
1.0
|
N5
|
A:NZ0305
|
4.4
|
24.6
|
1.0
|
CB
|
A:SER249
|
4.5
|
16.4
|
1.0
|
C3
|
A:NZ0305
|
4.5
|
26.3
|
1.0
|
CB
|
A:ASP124
|
4.6
|
15.1
|
1.0
|
CE1
|
A:HIS189
|
4.6
|
15.5
|
1.0
|
O1
|
A:NZ0305
|
4.7
|
19.9
|
1.0
|
CA
|
A:CYS208
|
4.7
|
16.1
|
1.0
|
OG
|
A:SER249
|
4.7
|
16.4
|
1.0
|
NE2
|
A:HIS120
|
4.8
|
16.1
|
1.0
|
CE1
|
A:HIS120
|
4.8
|
17.2
|
1.0
|
|
Cadmium binding site 4 out
of 6 in 7up3
Go back to
Cadmium Binding Sites List in 7up3
Cadmium binding site 4 out
of 6 in the NDM1-Inhibitor Co-Structure
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd301
b:19.8
occ:1.00
|
OD2
|
B:ASP223
|
2.2
|
18.8
|
1.0
|
OE2
|
B:GLU152
|
2.3
|
19.6
|
1.0
|
OE2
|
A:GLU227
|
2.3
|
26.5
|
1.0
|
O
|
B:HOH539
|
2.3
|
30.8
|
1.0
|
OE1
|
A:GLU227
|
2.4
|
27.0
|
1.0
|
OE1
|
B:GLU152
|
2.5
|
19.5
|
1.0
|
CD
|
A:GLU227
|
2.7
|
24.8
|
1.0
|
CD
|
B:GLU152
|
2.7
|
18.4
|
1.0
|
CG
|
B:ASP223
|
3.0
|
18.8
|
1.0
|
OD1
|
B:ASP223
|
3.1
|
22.3
|
1.0
|
NE2
|
B:HIS122
|
4.2
|
16.7
|
1.0
|
CG
|
A:GLU227
|
4.2
|
22.6
|
1.0
|
CG
|
B:GLU152
|
4.2
|
16.2
|
1.0
|
NE2
|
A:HIS228
|
4.2
|
18.8
|
1.0
|
O
|
B:HOH512
|
4.3
|
19.3
|
1.0
|
O
|
A:HOH432
|
4.4
|
45.3
|
1.0
|
CB
|
B:ASP223
|
4.4
|
16.2
|
1.0
|
O
|
B:HOH489
|
4.4
|
29.8
|
1.0
|
CE1
|
A:HIS228
|
4.5
|
18.4
|
1.0
|
O
|
B:HOH438
|
4.6
|
22.0
|
1.0
|
CD2
|
B:HIS122
|
4.7
|
15.8
|
1.0
|
O
|
A:HOH473
|
4.8
|
23.3
|
1.0
|
|
Cadmium binding site 5 out
of 6 in 7up3
Go back to
Cadmium Binding Sites List in 7up3
Cadmium binding site 5 out
of 6 in the NDM1-Inhibitor Co-Structure
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd302
b:20.2
occ:0.70
|
O
|
B:HOH473
|
2.3
|
26.8
|
1.0
|
OD2
|
B:ASP95
|
2.3
|
21.3
|
1.0
|
OD2
|
B:ASP130
|
2.3
|
27.3
|
1.0
|
O
|
B:HOH484
|
2.4
|
17.0
|
1.0
|
O
|
B:HOH550
|
2.4
|
24.8
|
1.0
|
CG
|
B:ASP95
|
3.2
|
19.5
|
1.0
|
CG
|
B:ASP130
|
3.2
|
25.1
|
1.0
|
OD1
|
B:ASP95
|
3.3
|
20.0
|
1.0
|
CB
|
B:ASP130
|
3.6
|
16.6
|
1.0
|
O
|
B:HOH423
|
4.1
|
20.9
|
1.0
|
O
|
B:GLY127
|
4.2
|
16.5
|
1.0
|
O
|
B:HOH492
|
4.3
|
24.1
|
1.0
|
OD1
|
B:ASP130
|
4.3
|
25.9
|
1.0
|
O
|
B:HOH563
|
4.4
|
28.6
|
1.0
|
O
|
B:HOH461
|
4.4
|
21.1
|
1.0
|
N
|
B:ASP130
|
4.5
|
14.8
|
1.0
|
O
|
B:HOH465
|
4.5
|
15.3
|
1.0
|
CB
|
B:ASP95
|
4.6
|
17.8
|
1.0
|
CG2
|
B:VAL155
|
4.6
|
20.6
|
1.0
|
CA
|
B:ASP130
|
4.7
|
14.9
|
1.0
|
|
Cadmium binding site 6 out
of 6 in 7up3
Go back to
Cadmium Binding Sites List in 7up3
Cadmium binding site 6 out
of 6 in the NDM1-Inhibitor Co-Structure
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd304
b:16.6
occ:1.00
|
OD2
|
B:ASP124
|
2.2
|
18.6
|
1.0
|
N3
|
B:NZ0305
|
2.2
|
19.6
|
1.0
|
NE2
|
B:HIS250
|
2.3
|
16.3
|
1.0
|
N4
|
B:NZ0305
|
2.4
|
17.1
|
1.0
|
SG
|
B:CYS208
|
2.5
|
16.2
|
1.0
|
N2
|
B:NZ0305
|
3.2
|
17.5
|
1.0
|
CG
|
B:ASP124
|
3.2
|
18.2
|
1.0
|
CD2
|
B:HIS250
|
3.2
|
16.4
|
1.0
|
C5
|
B:NZ0305
|
3.3
|
22.1
|
1.0
|
CE1
|
B:HIS250
|
3.3
|
16.7
|
1.0
|
S
|
B:NZ0305
|
3.5
|
18.3
|
1.0
|
C4
|
B:NZ0305
|
3.5
|
21.6
|
1.0
|
CB
|
B:CYS208
|
3.5
|
12.6
|
1.0
|
C6
|
B:NZ0305
|
3.6
|
19.5
|
1.0
|
OD1
|
B:ASP124
|
3.6
|
17.4
|
1.0
|
ZN
|
B:ZN303
|
3.7
|
15.5
|
1.0
|
O
|
B:NZ0305
|
4.1
|
17.8
|
1.0
|
N1
|
B:NZ0305
|
4.3
|
20.1
|
1.0
|
NE2
|
B:HIS189
|
4.4
|
13.3
|
1.0
|
N
|
B:NZ0305
|
4.4
|
20.4
|
1.0
|
CB
|
B:SER249
|
4.4
|
12.5
|
1.0
|
CG
|
B:HIS250
|
4.4
|
16.5
|
1.0
|
ND1
|
B:HIS250
|
4.4
|
16.2
|
1.0
|
N5
|
B:NZ0305
|
4.4
|
21.8
|
1.0
|
C3
|
B:NZ0305
|
4.5
|
25.1
|
1.0
|
CB
|
B:ASP124
|
4.5
|
14.2
|
1.0
|
CE1
|
B:HIS189
|
4.6
|
13.8
|
1.0
|
O1
|
B:NZ0305
|
4.7
|
21.1
|
1.0
|
CA
|
B:CYS208
|
4.7
|
13.3
|
1.0
|
OG
|
B:SER249
|
4.7
|
13.2
|
1.0
|
NE2
|
B:HIS120
|
4.7
|
13.6
|
1.0
|
CE1
|
B:HIS120
|
4.7
|
14.9
|
1.0
|
|
Reference:
M.Mandal,
L.Xiao,
W.Pan,
G.Scapin,
G.Li,
H.Tang,
S.W.Yang,
J.Pan,
Y.Root,
R.K.De Jesus,
C.Yang,
W.Prosise,
P.Dayananth,
A.Mirza,
A.G.Therien,
K.Young,
A.Flattery,
C.Garlisi,
R.Zhang,
D.Chu,
P.Sheth,
I.Chu,
J.Wu,
C.Markgraf,
H.Y.Kim,
R.Painter,
T.W.Mayhood,
E.Dinunzio,
D.F.Wyss,
A.V.Buevich,
T.Fischmann,
A.Pasternak,
S.Dong,
J.D.Hicks,
A.Villafania,
L.Liang,
N.Murgolo,
T.Black,
W.K.Hagmann,
J.Tata,
E.R.Parmee,
A.E.Weber,
J.Su,
H.Tang.
Rapid Evolution of A Fragment-Like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads Toward Clinical Candidates. J.Med.Chem. V. 65 16234 2022.
ISSN: ISSN 0022-2623
PubMed: 36475645
DOI: 10.1021/ACS.JMEDCHEM.2C00766
Page generated: Fri Jul 19 20:14:25 2024
|