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Chlorine in PDB 5x1w: PKM2 in Complex with Compound 5

Enzymatic activity of PKM2 in Complex with Compound 5

All present enzymatic activity of PKM2 in Complex with Compound 5:
2.7.1.40;

Protein crystallography data

The structure of PKM2 in Complex with Compound 5, PDB code: 5x1w was solved by Y.Matsui, H.Hanzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.823, 153.486, 94.207, 90.00, 103.52, 90.00
R / Rfree (%) 23.7 / 29

Chlorine Binding Sites:

The binding sites of Chlorine atom in the PKM2 in Complex with Compound 5 (pdb code 5x1w). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the PKM2 in Complex with Compound 5, PDB code: 5x1w:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5x1w

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Chlorine binding site 1 out of 8 in the PKM2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of PKM2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:31.4
occ:1.00
CL1 B:7Y0601 0.0 31.4 1.0
C15 B:7Y0601 1.7 32.3 1.0
C5 B:7Y0601 2.7 31.8 1.0
C17 B:7Y0601 2.7 32.3 1.0
CL3 B:7Y0601 3.1 32.0 1.0
OE1 B:GLU397 3.1 39.6 1.0
CD1 A:PHE26 3.6 39.7 1.0
CB A:PHE26 3.7 40.0 1.0
CD B:GLU397 3.7 39.9 1.0
N A:LEU27 3.8 40.8 1.0
C1 B:7Y0601 3.9 31.5 1.0
CD1 B:LEU394 4.0 33.4 1.0
C11 B:7Y0601 4.0 32.5 1.0
CG A:PHE26 4.0 39.8 1.0
OE2 B:GLU397 4.1 40.2 1.0
CB A:LEU27 4.2 40.7 1.0
CA B:LEU394 4.2 33.6 1.0
C A:PHE26 4.3 40.7 1.0
CA A:LEU27 4.3 40.7 1.0
CG B:GLN393 4.4 34.0 1.0
C3 B:7Y0601 4.5 31.8 1.0
CA A:PHE26 4.5 40.6 1.0
CB B:LEU394 4.6 33.5 1.0
CE1 A:PHE26 4.6 39.1 1.0
N B:LEU394 4.7 33.7 1.0
CB B:GLU397 4.7 39.1 1.0
CG B:GLU397 4.7 39.7 1.0
NE2 B:GLN393 4.7 34.1 1.0
CD B:GLN393 4.8 34.0 1.0
CG B:LEU394 4.9 33.4 1.0
CD1 A:LEU27 5.0 40.1 1.0
N A:PHE26 5.0 41.2 1.0
C B:GLN393 5.0 33.9 1.0
O B:GLN393 5.0 33.9 1.0

Chlorine binding site 2 out of 8 in 5x1w

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Chlorine binding site 2 out of 8 in the PKM2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of PKM2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:36.7
occ:1.00
CL2 B:7Y0601 0.0 36.7 1.0
C16 B:7Y0601 1.7 35.8 1.0
C6 B:7Y0601 2.7 35.3 1.0
C18 B:7Y0601 2.7 35.4 1.0
CL4 B:7Y0601 3.1 36.9 1.0
OE1 A:GLU397 3.2 37.2 1.0
CD1 B:PHE26 3.6 33.8 1.0
CB B:PHE26 3.7 34.0 1.0
N B:LEU27 3.8 34.3 1.0
CD1 A:LEU394 3.9 33.9 1.0
C2 B:7Y0601 3.9 34.2 1.0
C12 B:7Y0601 4.0 34.5 1.0
CD A:GLU397 4.0 37.9 1.0
CG B:PHE26 4.1 33.9 1.0
CB B:LEU27 4.1 34.5 1.0
CA B:LEU27 4.2 34.3 1.0
C B:PHE26 4.3 34.1 1.0
CA A:LEU394 4.3 35.4 1.0
C4 B:7Y0601 4.5 34.3 1.0
CA B:PHE26 4.5 34.1 1.0
CB A:LEU394 4.6 34.8 1.0
OE2 A:GLU397 4.6 38.2 1.0
CE1 B:PHE26 4.7 33.7 1.0
CB A:GLU397 4.7 38.0 1.0
N A:LEU394 4.8 36.0 1.0
CG A:GLN393 4.9 36.0 1.0
CG A:GLU397 4.9 38.4 1.0
CG A:LEU394 4.9 34.2 1.0
O B:PHE26 4.9 34.0 1.0

Chlorine binding site 3 out of 8 in 5x1w

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Chlorine binding site 3 out of 8 in the PKM2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of PKM2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:32.0
occ:1.00
CL3 B:7Y0601 0.0 32.0 1.0
C17 B:7Y0601 1.7 32.3 1.0
C15 B:7Y0601 2.7 32.3 1.0
C11 B:7Y0601 2.7 32.5 1.0
C21 B:7Y0601 3.1 32.7 1.0
CL1 B:7Y0601 3.1 31.4 1.0
O33 B:7Y0601 3.2 31.3 1.0
O B:TYR390 3.6 33.6 1.0
CG B:GLN393 3.7 34.0 1.0
CD B:GLN393 3.9 34.0 1.0
N B:LEU394 3.9 33.7 1.0
CB B:GLN393 4.0 34.0 1.0
C5 B:7Y0601 4.0 31.8 1.0
C3 B:7Y0601 4.0 31.8 1.0
OE1 B:GLN393 4.0 34.0 1.0
C13 B:7Y0601 4.1 33.2 1.0
CB B:LEU394 4.1 33.5 1.0
CB B:TYR390 4.2 33.7 1.0
CE2 B:PHE26 4.2 33.7 1.0
CA B:LEU394 4.2 33.6 1.0
CD2 B:PHE26 4.4 33.8 1.0
CD2 B:TYR390 4.5 33.9 1.0
C B:GLN393 4.5 33.9 1.0
C1 B:7Y0601 4.5 31.5 1.0
CD1 A:PHE26 4.5 39.7 1.0
C B:TYR390 4.6 33.6 1.0
NE2 B:GLN393 4.6 34.1 1.0
CG B:TYR390 4.7 33.9 1.0
C9 B:7Y0601 4.7 33.4 1.0
CA B:GLN393 4.8 34.0 1.0
CA B:TYR390 4.9 33.7 1.0
CG A:PHE26 5.0 39.8 1.0
CD1 B:LEU394 5.0 33.4 1.0

Chlorine binding site 4 out of 8 in 5x1w

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Chlorine binding site 4 out of 8 in the PKM2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of PKM2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:36.9
occ:1.00
CL4 B:7Y0601 0.0 36.9 1.0
C18 B:7Y0601 1.7 35.4 1.0
C16 B:7Y0601 2.7 35.8 1.0
C12 B:7Y0601 2.7 34.5 1.0
C22 B:7Y0601 3.1 33.8 1.0
CL2 B:7Y0601 3.1 36.7 1.0
O34 B:7Y0601 3.2 33.0 1.0
O A:TYR390 3.7 38.4 1.0
CB A:GLN393 3.9 36.5 1.0
N A:LEU394 3.9 36.0 1.0
CG A:GLN393 4.0 36.0 1.0
C6 B:7Y0601 4.0 35.3 1.0
C4 B:7Y0601 4.0 34.3 1.0
CB A:LEU394 4.0 34.8 1.0
CD A:GLN393 4.1 35.9 1.0
C14 B:7Y0601 4.1 33.0 1.0
CA A:LEU394 4.2 35.4 1.0
OE1 A:GLN393 4.2 36.0 1.0
CE2 A:PHE26 4.3 39.1 1.0
CB A:TYR390 4.4 37.9 1.0
C A:GLN393 4.5 36.5 1.0
CD1 B:PHE26 4.5 33.8 1.0
C2 B:7Y0601 4.5 34.2 1.0
CD2 A:PHE26 4.5 39.4 1.0
NE2 A:GLN393 4.6 35.5 1.0
C A:TYR390 4.7 38.2 1.0
CD2 A:TYR390 4.7 38.6 1.0
CA A:GLN393 4.8 36.8 1.0
C10 B:7Y0601 4.8 32.1 1.0
CG B:PHE26 4.9 33.9 1.0
CD1 A:LEU394 4.9 33.9 1.0
CE1 B:PHE26 5.0 33.7 1.0
CG A:LEU394 5.0 34.2 1.0
CB B:PHE26 5.0 34.0 1.0

Chlorine binding site 5 out of 8 in 5x1w

Go back to Chlorine Binding Sites List in 5x1w
Chlorine binding site 5 out of 8 in the PKM2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of PKM2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:29.4
occ:1.00
CL1 C:7Y0601 0.0 29.4 1.0
C15 C:7Y0601 1.7 29.8 1.0
C5 C:7Y0601 2.7 30.0 1.0
C17 C:7Y0601 2.7 30.0 1.0
CL3 C:7Y0601 3.1 30.6 1.0
OE1 D:GLU397 3.2 40.0 1.0
CD1 C:PHE26 3.6 36.0 1.0
CB C:PHE26 3.7 36.9 1.0
CD D:GLU397 3.8 40.5 1.0
N C:LEU27 3.9 38.2 1.0
C11 C:7Y0601 4.0 30.0 1.0
C1 C:7Y0601 4.0 29.8 1.0
CG C:PHE26 4.0 36.2 1.0
CD1 D:LEU394 4.1 34.3 1.0
CA D:LEU394 4.2 35.2 1.0
C C:PHE26 4.3 37.8 1.0
OE2 D:GLU397 4.3 40.9 1.0
CB C:LEU27 4.4 38.8 1.0
CG D:GLN393 4.4 34.6 1.0
CA C:LEU27 4.4 38.5 1.0
C3 C:7Y0601 4.5 29.9 1.0
CA C:PHE26 4.5 37.3 1.0
CB D:LEU394 4.6 34.7 1.0
N D:LEU394 4.6 35.0 1.0
CG D:GLU397 4.6 40.6 1.0
CE1 C:PHE26 4.6 35.3 1.0
CB D:GLU397 4.7 40.4 1.0
O D:GLN393 4.9 35.5 1.0
C D:GLN393 4.9 35.0 1.0
CG D:LEU394 4.9 34.3 1.0
CD D:GLN393 4.9 34.8 1.0
NE2 D:GLN393 5.0 34.9 1.0

Chlorine binding site 6 out of 8 in 5x1w

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Chlorine binding site 6 out of 8 in the PKM2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of PKM2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:41.0
occ:1.00
CL2 C:7Y0601 0.0 41.0 1.0
C16 C:7Y0601 1.7 40.0 1.0
C6 C:7Y0601 2.7 40.3 1.0
C18 C:7Y0601 2.7 38.4 1.0
CL4 C:7Y0601 3.1 36.8 1.0
OE1 C:GLU397 3.2 43.3 1.0
N D:LEU27 3.6 37.5 1.0
CD1 D:PHE26 3.6 36.1 1.0
CB D:PHE26 3.8 36.6 1.0
C2 C:7Y0601 4.0 39.9 1.0
C12 C:7Y0601 4.0 38.2 1.0
CD C:GLU397 4.0 43.1 1.0
CB D:LEU27 4.0 38.1 1.0
CD1 C:LEU394 4.0 36.2 1.0
CA D:LEU27 4.1 37.7 1.0
CG D:PHE26 4.1 36.0 1.0
C D:PHE26 4.2 37.1 1.0
CA C:LEU394 4.3 36.8 1.0
C4 C:7Y0601 4.5 38.5 1.0
CA D:PHE26 4.5 37.1 1.0
OE2 C:GLU397 4.5 43.2 1.0
CB C:LEU394 4.6 36.3 1.0
CE1 D:PHE26 4.7 35.3 1.0
CG C:GLN393 4.7 34.9 1.0
N C:LEU394 4.8 36.7 1.0
O D:PHE26 4.8 36.9 1.0
CB C:GLU397 4.8 41.6 1.0
CG C:GLU397 4.9 42.5 1.0
CD1 D:LEU27 4.9 37.8 1.0
NE2 C:GLN393 4.9 34.8 1.0
N D:PHE26 4.9 38.4 1.0
CG D:LEU27 5.0 38.3 1.0
CG C:LEU394 5.0 36.0 1.0

Chlorine binding site 7 out of 8 in 5x1w

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Chlorine binding site 7 out of 8 in the PKM2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of PKM2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:30.6
occ:1.00
CL3 C:7Y0601 0.0 30.6 1.0
C17 C:7Y0601 1.7 30.0 1.0
C15 C:7Y0601 2.7 29.8 1.0
C11 C:7Y0601 2.7 30.0 1.0
C21 C:7Y0601 3.1 29.9 1.0
CL1 C:7Y0601 3.1 29.4 1.0
O33 C:7Y0601 3.2 30.1 1.0
O D:TYR390 3.7 33.8 1.0
CG D:GLN393 3.8 34.6 1.0
N D:LEU394 3.9 35.0 1.0
CB D:GLN393 3.9 34.5 1.0
C5 C:7Y0601 4.0 30.0 1.0
C3 C:7Y0601 4.0 29.9 1.0
CE2 D:PHE26 4.1 34.9 1.0
CB D:LEU394 4.1 34.7 1.0
C13 C:7Y0601 4.1 30.1 1.0
CA D:LEU394 4.2 35.2 1.0
CD D:GLN393 4.2 34.8 1.0
CB D:TYR390 4.2 34.1 1.0
CD2 D:PHE26 4.3 35.4 1.0
OE1 D:GLN393 4.4 34.8 1.0
C D:GLN393 4.4 35.0 1.0
C1 C:7Y0601 4.5 29.8 1.0
CD2 D:TYR390 4.5 34.5 1.0
CD1 C:PHE26 4.5 36.0 1.0
C D:TYR390 4.7 33.9 1.0
CA D:GLN393 4.7 34.9 1.0
CG D:TYR390 4.8 34.4 1.0
C9 C:7Y0601 4.9 30.1 1.0
CG C:PHE26 4.9 36.2 1.0
CA D:TYR390 4.9 33.9 1.0
CE1 C:PHE26 4.9 35.3 1.0
NE2 D:GLN393 4.9 34.9 1.0

Chlorine binding site 8 out of 8 in 5x1w

Go back to Chlorine Binding Sites List in 5x1w
Chlorine binding site 8 out of 8 in the PKM2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of PKM2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:36.8
occ:1.00
CL4 C:7Y0601 0.0 36.8 1.0
C18 C:7Y0601 1.7 38.4 1.0
C16 C:7Y0601 2.7 40.0 1.0
C12 C:7Y0601 2.7 38.2 1.0
C22 C:7Y0601 3.1 37.1 1.0
CL2 C:7Y0601 3.1 41.0 1.0
O34 C:7Y0601 3.2 36.7 1.0
CG C:GLN393 3.8 34.9 1.0
O C:TYR390 3.9 35.1 1.0
N C:LEU394 3.9 36.7 1.0
CD C:GLN393 3.9 34.7 1.0
CB C:GLN393 4.0 35.5 1.0
C6 C:7Y0601 4.0 40.3 1.0
C4 C:7Y0601 4.0 38.5 1.0
CB C:LEU394 4.0 36.3 1.0
CA C:LEU394 4.1 36.8 1.0
OE1 C:GLN393 4.1 34.6 1.0
C14 C:7Y0601 4.1 35.0 1.0
CE2 C:PHE26 4.2 35.2 1.0
CD1 D:PHE26 4.3 36.1 1.0
CB C:TYR390 4.4 34.5 1.0
C C:GLN393 4.5 36.5 1.0
C2 C:7Y0601 4.5 39.9 1.0
NE2 C:GLN393 4.5 34.8 1.0
CD2 C:PHE26 4.5 35.7 1.0
CD2 C:TYR390 4.6 35.0 1.0
CA C:GLN393 4.8 36.2 1.0
CG D:PHE26 4.8 36.0 1.0
C C:TYR390 4.9 34.8 1.0
CE1 D:PHE26 4.9 35.3 1.0
CD1 C:LEU394 4.9 36.2 1.0
CB D:PHE26 4.9 36.6 1.0
C8 C:7Y0601 5.0 33.3 1.0
CG C:TYR390 5.0 34.8 1.0
CG C:LEU394 5.0 36.0 1.0

Reference:

Y.Matsui, I.Yasumatsu, T.Asahi, T.Kitamura, K.Kanai, O.Ubukata, H.Hayasaka, S.Takaishi, H.Hanzawa, S.Katakura. Discovery and Structure-Guided Fragment-Linking of 4-(2,3-Dichlorobenzoyl)-1-Methyl-Pyrrole-2-Carboxamide As A Pyruvate Kinase M2 Activator Bioorg. Med. Chem. V. 25 3540 2017.
ISSN: ESSN 1464-3391
PubMed: 28511909
DOI: 10.1016/J.BMC.2017.05.004
Page generated: Fri Jul 26 20:45:29 2024

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