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Ytterbium 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
Chlorine (Cl) 7 atoms

Ytterbium Binding Sites:

The binding sites of Ytterbium 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 Ytterbium atom.
In total 2 binding sites of Ytterbium 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 Ytterbium binding site number: 1; 2;

Ytterbium binding site 1 out of 2 in 6dum

Go back to Ytterbium Binding Sites List in 6dum
Ytterbium binding site 1 out of 2 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 Ytterbium with other atoms in the Yb 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:Yb601

b:51.3
occ:1.00
 O A:HOH815 2.0 23.2 1.0
O A:HOH838 2.2 27.2 1.0
O A:HOH747 2.2 40.9 1.0
O A:HOH858 2.3 28.9 1.0
O A:HOH825 2.3 50.4 1.0
O A:HOH851 2.3 41.9 1.0
O A:HOH866 2.3 37.7 1.0
O A:HOH819 3.1 37.1 1.0
CL A:CL607 4.0 82.2 1.0
OE2 A:GLU46 4.2 67.8 1.0
O A:ASN377 4.5 63.4 1.0
O A:HOH708 4.5 40.0 1.0
OE1 A:GLU46 4.8 66.7 1.0
O A:HOH729 4.8 55.4 1.0
CD A:GLU46 4.9 65.2 1.0

Ytterbium binding site 2 out of 2 in 6dum

Go back to Ytterbium Binding Sites List in 6dum
Ytterbium binding site 2 out of 2 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 Ytterbium with other atoms in the Yb 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:Yb602

b:57.5
occ:1.00
 O A:HOH859 2.2 36.5 1.0
O1N A:NAI604 2.2 44.2 1.0
O A:HOH780 2.2 43.8 1.0
O2A A:NAI604 2.2 37.2 1.0
O A:HOH701 2.2 52.8 1.0
CL A:CL610 2.5 65.3 1.0
O A:HOH842 2.6 42.0 1.0
CL A:CL605 2.7 75.4 1.0
CL A:CL611 2.8 67.0 1.0
PN A:NAI604 3.6 49.6 1.0
PA A:NAI604 3.7 50.9 1.0
O3 A:NAI604 4.2 51.1 1.0
OE1 A:GLU349 4.4 55.3 1.0
CG2 A:VAL250 4.5 52.7 1.0
O2N A:NAI604 4.5 48.8 1.0
OE1 A:GLU249 4.5 74.5 1.0
O1A A:NAI604 4.6 47.0 1.0
O5D A:NAI604 4.7 54.2 1.0
OG A:SER247 4.7 52.6 1.0
C5D A:NAI604 4.7 48.8 1.0
C8A A:NAI604 4.7 45.7 1.0
O5B A:NAI604 4.7 45.7 1.0
OE2 A:GLU349 4.7 58.2 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 Oct 12 21:21:40 2024

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