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Magnesium in PDB 7u8h: Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit

Enzymatic activity of Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit

All present enzymatic activity of Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit:
3.6.5.2;

Protein crystallography data

The structure of Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit, PDB code: 7u8h was solved by J.Phan, S.W.Fesik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 1.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 94.835, 98.48, 149.888, 90, 90, 90
R / Rfree (%) 17.2 / 19.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit (pdb code 7u8h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit, PDB code: 7u8h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7u8h

Go back to Magnesium Binding Sites List in 7u8h
Magnesium binding site 1 out of 4 in the Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:13.7
occ:1.00
 O A:HOH328 2.1 14.0 1.0
O2B A:GDP202 2.1 10.6 1.0
O A:HOH357 2.1 14.0 1.0
OG A:SER17 2.1 13.5 1.0
O A:HOH344 2.1 14.8 1.0
O A:HOH338 2.2 13.9 1.0
CB A:SER17 3.2 13.7 1.0
PB A:GDP202 3.3 12.2 1.0
O3B A:GDP202 3.6 13.1 1.0
N A:SER17 4.0 13.8 1.0
OD2 A:ASP57 4.1 20.7 1.0
O2A A:GDP202 4.1 15.6 1.0
CA A:SER17 4.1 15.5 1.0
CD2 A:TYR32 4.2 27.2 1.0
OD1 A:ASP57 4.2 18.1 1.0
O A:ASP33 4.3 24.5 1.0
O1B A:GDP202 4.3 12.0 1.0
O3A A:GDP202 4.4 12.7 1.0
O A:PRO34 4.4 22.2 1.0
CA A:PRO34 4.4 24.4 1.0
O A:THR58 4.5 23.1 1.0
O A:ILE36 4.5 18.2 1.0
CE2 A:TYR32 4.6 25.3 1.0
PA A:GDP202 4.6 13.4 1.0
CG A:ASP57 4.6 16.5 1.0
C A:PRO34 4.7 25.9 1.0
O A:HOH349 4.7 23.5 1.0
O1A A:GDP202 4.7 12.9 1.0
O A:TYR32 4.9 28.6 1.0
CB A:LYS16 5.0 10.0 1.0

Magnesium binding site 2 out of 4 in 7u8h

Go back to Magnesium Binding Sites List in 7u8h
Magnesium binding site 2 out of 4 in the Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:15.2
occ:1.00
 O B:HOH323 2.0 15.4 1.0
O3B B:GDP202 2.0 15.2 1.0
O B:HOH347 2.0 18.6 1.0
OG B:SER17 2.1 16.5 1.0
O B:HOH337 2.2 21.3 1.0
O B:HOH322 2.2 17.1 1.0
CB B:SER17 3.1 19.3 1.0
PB B:GDP202 3.3 13.8 1.0
O2B B:GDP202 3.5 15.7 1.0
N B:SER17 3.9 15.0 1.0
CA B:SER17 4.1 15.4 1.0
OD2 B:ASP57 4.1 29.8 1.0
O1A B:GDP202 4.1 18.1 1.0
O B:PRO34 4.2 28.5 1.0
O B:ASP33 4.3 28.6 1.0
OD1 B:ASP57 4.3 25.8 1.0
O1B B:GDP202 4.3 12.2 1.0
CB B:ALA59 4.3 25.7 1.0
O3A B:GDP202 4.4 14.7 1.0
CD2 B:TYR32 4.4 31.2 1.0
CA B:PRO34 4.5 26.2 1.0
O B:THR58 4.5 21.1 1.0
O B:ILE36 4.5 25.7 0.5
O B:ILE36 4.5 25.7 0.6
PA B:GDP202 4.6 18.4 1.0
CG B:ASP57 4.6 29.4 1.0
O2A B:GDP202 4.6 18.9 1.0
C B:PRO34 4.6 26.8 1.0
CE2 B:TYR32 4.8 40.0 1.0
CE B:LYS16 4.8 17.1 1.0
CB B:LYS16 4.8 13.1 1.0
C B:LYS16 4.9 13.4 1.0
NZ B:LYS16 5.0 15.7 1.0

Magnesium binding site 3 out of 4 in 7u8h

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Magnesium binding site 3 out of 4 in the Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:26.7
occ:1.00
 O2B C:GDP202 2.0 22.5 1.0
O C:HOH308 2.2 25.1 1.0
O C:HOH338 2.2 21.9 1.0
O C:HOH322 2.2 27.4 1.0
OG C:SER17 2.3 26.2 1.0
PB C:GDP202 3.1 27.1 1.0
O3B C:GDP202 3.3 30.5 1.0
CB C:SER17 3.6 26.9 1.0
O C:PRO34 3.8 40.8 1.0
CA C:PRO34 4.0 43.5 1.0
O2A C:GDP202 4.0 28.8 1.0
O1B C:GDP202 4.1 26.6 1.0
C C:PRO34 4.1 41.4 1.0
O C:THR58 4.2 30.1 1.0
O C:HOH354 4.2 36.1 1.0
N C:SER17 4.3 25.1 1.0
O C:ASP33 4.3 44.5 1.0
O3A C:GDP202 4.3 32.7 1.0
O C:HOH301 4.5 33.8 1.0
CA C:SER17 4.5 28.4 1.0
CD2 C:TYR32 4.5 59.1 1.0
O C:ILE36 4.5 40.7 1.0
CB C:ALA59 4.5 37.4 1.0
OD2 C:ASP57 4.6 27.0 1.0
PA C:GDP202 4.6 27.1 1.0
OD1 C:ASP57 4.6 24.1 1.0
O C:HOH312 4.7 39.5 1.0
CE2 C:TYR32 4.7 57.5 1.0
NZ C:LYS16 4.7 25.3 1.0
O C:HOH306 4.8 46.1 1.0
CE C:LYS16 4.8 30.0 1.0
N C:PRO34 4.9 44.0 1.0
C C:ASP33 5.0 46.5 1.0

Magnesium binding site 4 out of 4 in 7u8h

Go back to Magnesium Binding Sites List in 7u8h
Magnesium binding site 4 out of 4 in the Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Discovery of A Kras G12V Inhibitor in Vivo Tool Compound Starting From An Hsqc-uc(Nmr) Based Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:9.6
occ:1.00
 O2B D:GDP202 2.0 9.2 1.0
OG D:SER17 2.1 11.3 1.0
O D:HOH320 2.1 11.1 1.0
O D:HOH325 2.1 11.0 1.0
O D:HOH352 2.2 12.5 1.0
O D:HOH329 2.2 11.3 1.0
CB D:SER17 3.2 12.7 1.0
PB D:GDP202 3.3 7.8 1.0
O3B D:GDP202 3.5 10.1 1.0
N D:SER17 3.9 8.2 1.0
CA D:SER17 4.1 9.3 1.0
OD2 D:ASP57 4.1 16.5 1.0
O2A D:GDP202 4.1 13.3 1.0
CD2 D:TYR32 4.2 19.4 1.0
OD1 D:ASP57 4.2 17.9 1.0
O D:PRO34 4.2 17.2 1.0
O D:ASP33 4.3 18.1 1.0
O1B D:GDP202 4.3 8.0 1.0
O3A D:GDP202 4.3 7.6 1.0
CA D:PRO34 4.5 16.2 1.0
O D:THR58 4.5 21.1 1.0
O D:ILE36 4.6 16.7 1.0
PA D:GDP202 4.6 9.9 1.0
O1A D:GDP202 4.6 12.0 1.0
CG D:ASP57 4.6 21.9 1.0
C D:PRO34 4.6 13.9 1.0
CE2 D:TYR32 4.7 20.4 1.0
O D:TYR32 4.8 21.3 1.0
CE D:LYS16 4.9 10.6 1.0
CB D:LYS16 4.9 7.3 1.0
O D:HOH371 4.9 13.1 1.0
C D:LYS16 5.0 7.7 1.0

Reference:

J.Broker, A.G.Waterson, C.Smethurst, D.Kessler, J.Bottcher, M.Mayer, G.Gmaschitz, J.Phan, A.Little, J.R.Abbott, Q.Sun, M.Gmachl, D.Rudolph, H.Arnhof, K.Rumpel, F.Savarese, T.Gerstberger, N.Mischerikow, M.Treu, L.Herdeis, T.Wunberg, A.Gollner, H.Weinstabl, A.Mantoulidis, O.Kramer, D.B.Mcconnell, S.W Fesik. Fragment Optimization of Reversible Binding to the Switch II Pocket on Kras Leads to A Potent, in Vivo Active Kras G12C Inhibitor. J.Med.Chem. V. 65 14614 2022.
ISSN: ISSN 0022-2623
PubMed: 36300829
DOI: 10.1021/ACS.JMEDCHEM.2C01120
Page generated: Thu Oct 3 09:52:14 2024

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