Atomistry » Ytterbium » PDB 5l2m-8t0t » 6dum
Atomistry »
  Ytterbium »
    PDB 5l2m-8t0t »
      6dum »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy