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Chlorine in PDB 6dum: ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)

Enzymatic activity of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)

All present enzymatic activity of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G):
1.2.1.36;

Protein crystallography data

The structure of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G), PDB code: 6dum was solved by C.D.Buchman, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 108.802, 108.802, 82.877, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.9

Other elements in 6dum:

The structure of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) also contains other interesting chemical elements:

Fluorine (F) 1 atom
Ytterbium (Yb) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) (pdb code 6dum). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G), PDB code: 6dum:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6dum

Go back to Chlorine Binding Sites List in 6dum
Chlorine binding site 1 out of 7 in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:75.4
occ:1.00
 O1N A:NAI604 2.2 44.2 1.0
OE2 A:GLU349 2.3 58.2 1.0
OE1 A:GLU349 2.5 55.3 1.0
CL A:CL611 2.6 67.0 1.0
CL A:CL610 2.6 65.3 1.0
CD A:GLU349 2.7 55.5 1.0
YB A:YB602 2.7 57.5 1.0
PN A:NAI604 3.3 49.6 1.0
O2N A:NAI604 3.6 48.8 1.0
O A:HOH859 3.8 36.5 1.0
O5D A:NAI604 4.0 54.2 1.0
O2A A:NAI604 4.0 37.2 1.0
O A:HOH701 4.0 52.8 1.0
CG A:GLU349 4.1 54.0 1.0
O A:HOH842 4.1 42.0 1.0
C5D A:NAI604 4.2 48.8 1.0
CB A:GLU349 4.7 53.0 1.0
O3 A:NAI604 4.7 51.1 1.0
O A:HOH780 4.8 43.8 1.0

Chlorine binding site 2 out of 7 in 6dum

Go back to Chlorine Binding Sites List in 6dum
Chlorine binding site 2 out of 7 in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl606

b:59.7
occ:1.00
 OD1 A:ASP283 2.7 63.0 1.0
OD2 A:ASP283 2.9 64.2 1.0
CG A:ASP283 3.2 60.6 1.0
O A:HOH835 3.6 53.0 1.0
CB A:ASP285 4.1 61.2 1.0
N A:ASN286 4.3 53.1 1.0
CB A:ASN286 4.6 51.0 1.0
CB A:ASP283 4.7 58.7 1.0
OD2 A:ASP285 4.8 72.2 1.0
CA A:ASP285 4.9 58.5 1.0
CA A:ASN286 4.9 51.5 1.0
C A:ASP285 4.9 54.1 1.0

Chlorine binding site 3 out of 7 in 6dum

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Chlorine binding site 3 out of 7 in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl607

b:82.2
occ:1.00
 O A:HOH747 3.0 40.9 1.0
O A:HOH825 3.4 50.4 1.0
CE A:LYS378 4.0 76.0 1.0
O A:HOH858 4.0 28.9 1.0
OE1 A:GLU46 4.0 66.7 1.0
YB A:YB601 4.0 51.3 1.0
O A:ASN377 4.1 63.4 1.0
OE2 A:GLU46 4.4 67.8 1.0
CD A:GLU46 4.5 65.2 1.0
NZ A:LYS378 4.6 77.5 1.0
O A:HOH815 4.8 23.2 1.0
O A:HOH838 4.8 27.2 1.0
CD A:LYS378 5.0 74.0 1.0
CG A:LYS378 5.0 69.6 1.0

Chlorine binding site 4 out of 7 in 6dum

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Chlorine binding site 4 out of 7 in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl608

b:86.1
occ:0.50
 CB A:HIS484 3.7 54.0 1.0
OE1 A:GLU485 4.0 82.0 1.0
OH A:TYR481 4.2 53.8 1.0
CG A:HIS484 4.3 55.7 1.0
CD A:GLU485 4.5 71.3 1.0
CZ A:TYR481 4.5 48.9 1.0
CD2 A:HIS484 4.5 54.0 1.0
CE2 A:TYR481 4.6 47.4 1.0
OE2 A:GLU485 4.6 71.0 1.0
C A:HIS484 5.0 51.0 1.0
CA A:HIS484 5.0 51.5 1.0

Chlorine binding site 5 out of 7 in 6dum

Go back to Chlorine Binding Sites List in 6dum
Chlorine binding site 5 out of 7 in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl609

b:48.5
occ:1.00
 NE2 A:HIS157 3.1 43.7 1.0
OG1 A:THR155 3.2 40.8 1.0
CG2 A:THR155 3.7 39.7 1.0
CB A:THR155 3.7 40.7 1.0
CG A:ARG143 3.9 43.3 1.0
CE1 A:HIS157 4.0 42.3 1.0
CG1 A:VAL489 4.0 43.0 1.0
CD2 A:HIS157 4.1 43.5 1.0
CB A:ARG143 4.3 43.4 1.0
N A:ARG143 4.8 40.5 1.0
CG2 A:VAL489 4.9 46.3 1.0
CD1 A:ILE145 5.0 42.0 1.0

Chlorine binding site 6 out of 7 in 6dum

Go back to Chlorine Binding Sites List in 6dum
Chlorine binding site 6 out of 7 in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl610

b:65.3
occ:1.00
 O A:HOH859 2.4 36.5 1.0
YB A:YB602 2.5 57.5 1.0
OE1 A:GLU349 2.6 55.3 1.0
CL A:CL605 2.6 75.4 1.0
CL A:CL611 2.8 67.0 1.0
CD A:GLU349 3.4 55.5 1.0
O A:HOH701 3.5 52.8 1.0
O1N A:NAI604 3.5 44.2 1.0
OE2 A:GLU349 3.6 58.2 1.0
O A:HOH780 3.7 43.8 1.0
O A:HOH842 4.5 42.0 1.0
O2A A:NAI604 4.6 37.2 1.0
CG A:GLU349 4.7 54.0 1.0
OE1 A:GLU249 4.9 74.5 1.0
C5D A:NAI604 5.0 48.8 1.0
PN A:NAI604 5.0 49.6 1.0

Chlorine binding site 7 out of 7 in 6dum

Go back to Chlorine Binding Sites List in 6dum
Chlorine binding site 7 out of 7 in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl611

b:67.0
occ:1.00
 O A:HOH859 2.4 36.5 1.0
CL A:CL605 2.6 75.4 1.0
O A:HOH842 2.8 42.0 1.0
CL A:CL610 2.8 65.3 1.0
YB A:YB602 2.8 57.5 1.0
OE2 A:GLU349 3.2 58.2 1.0
CD A:GLU349 4.0 55.5 1.0
O1N A:NAI604 4.0 44.2 1.0
OE1 A:GLU349 4.0 55.3 1.0
O A:HOH780 4.1 43.8 1.0
O2A A:NAI604 4.6 37.2 1.0
O A:HOH701 4.9 52.8 1.0

Reference:

B.C.Huddle, E.Grimley, C.D.Buchman, M.Chtcherbinine, B.Debnath, P.Mehta, K.Yang, C.A.Morgan, S.Li, J.Felton, D.Sun, G.Mehta, N.Neamati, R.J.Buckanovich, T.D.Hurley, S.D.Larsen. Structure-Based Optimization of A Novel Class of Aldehyde Dehydrogenase 1A (ALDH1A) Subfamily-Selective Inhibitors As Potential Adjuncts to Ovarian Cancer Chemotherapy. J.Med.Chem. V. 61 8754 2018.
ISSN: ISSN 0022-2623
PubMed: 30221940
DOI: 10.1021/ACS.JMEDCHEM.8B00930
Page generated: Sat Jul 27 21:49:28 2024

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