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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:

Zinc (Zn) 2 atoms

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: Thu Jul 10 15:36:35 2025

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