Structure and Conformations of GABA-Transaminase Inhibitors. IV. Transition State Analogs

1988 ◽  
Vol 41 (4) ◽  
pp. 493 ◽  
Author(s):  
PR Andrews ◽  
JM Gulbis ◽  
MN Iskander ◽  
MF Mackay ◽  
C Dipaola ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Transition State ◽  
Crystal Structures ◽  
Minimum Energy ◽  
Low Energy ◽  
Gaba Transaminase ◽  
Transition State Analogs ◽  
Potential Inhibitors ◽  
Low Energy Conformations

Crystal structures of three potential inhibitors [salicylamide derivative C16H15NO4 (5), pyridoxazine C11H16N2O5S (6) and benzoxazone C12H13NO4 (7).H2O] of GABA- transaminase (E.C.2.6.1.19, GABA-T) based on the calculated transition state of GABA-T were determined. The conformational analyses of these structures (non-bonded energies, MNDO,AM1) indicate that they can all fit the transition state in relatively low energy conformations. The crystal structures appear to be close to the calculated minimum energy conformations, except for the salicylamide derivative (5), which features internal hydrogen-bonding. The AM1 parametrization has been used successfully to predict two possible hydrogen-bonded conformations of (5), one of which is found in the crystal structure.

Structure and Conformations of Gaba-Transaminase Inhibitors. II. Transition-State Analogs

1986 ◽  
Vol 39 (10) ◽  
pp. 1575 ◽  
Author(s):  
PR Andrews ◽  
V Cody ◽  
JM Gulbis ◽  
MN Iskander ◽  
AI Jeffrey ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Transition State ◽  
Crystal Structures ◽  
Gaba Transaminase ◽  
Preceding Article ◽  
Transition State Analogs ◽  
Calculated Energy ◽  
Transition State Analogue ◽  
Oxazine Ring ◽  
Transition State Analogue Inhibitors

Crystal structures of two benzoxazine derivatives designed as transition state analogue inhibitors of GABA-T were determined. These cyclic oxazine structures are shown to be more similar to the proposed transition state than the pyridoxal derivatives reported in the preceding article.1 Conformational analyses (non-bonded energy, MINDO/3, MNDO) show that the crystal structures are close to the calculated energy minima. The MNDO parameterization gives geometries close to the crystal structure, with the configuration at the nitrogen of the oxazine ring in particular being better reproduced than by the MINDO/3 method, which tends to prefer planar (sp2) nitrogen.

scholarly journals How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dariusz Czernecki ◽  
Pierre Legrand ◽  
Mustafa Tekpinar ◽  
Sandrine Rosario ◽  
Pierre-Alexandre Kaminski ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Active Site ◽  
Metal Ion ◽  
Restriction Endonucleases ◽  
Structural Element

AbstractBacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host’s restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 Å resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering.

Complexes of Copper, Silver, and Gold with Urea Homologues. Crystal Structures of [{µ2-SeC(NH2)2} Ag{SeC(NH2)2}2]22+2Cl- • 4 DMF and [Ph3PAu{SC(NHMe)2}]+Cl- • SC(NHMe)2

1994 ◽  
Vol 49 (1) ◽  
pp. 21-26 ◽  
Author(s):  
Wolfgang Eikens ◽  
Peter G. Jones ◽  
Jürgen Lautner ◽  
Carsten Thöne
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Dinuclear Complex ◽  
Selenium Atom

Abstract The title compounds were prepared from chloro(organophosphine)metal(I) complexes and the urea homologues SeC(NH2)2 and SC(NHMe)2 in good yields. Recrystallization of [Ph3,PAg{SeC(NH2)2}]+Cl- from DMF/CH2Cl2 leads in low yield to the dinuclear complex [{µ2-SeC(NH2)2}Ag{SeC(NH2)2}2]22+2Cl- • 4DMF. The crystal structure reveals short Ag-Ag contacts and unexpectedly acute angles at the bridging selenium atom. The crystal structure of [Ph3PAu{SC(NHMe)2}]+Cl- • SC(NHMe)2 shows short N•••Cl and N•••S contacts that probably correspond to hydrogen bonding.

Structure and Conformations of Gaba-Transaminase Inhibitors. I. Multisubstrate Analogs

1986 ◽  
Vol 39 (10) ◽  
pp. 1559
Author(s):  
PR Andrews ◽  
V Cody ◽  
MN Iskander ◽  
AI Jeffrey ◽  
MF Mackay ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Transition State ◽  
Intramolecular Hydrogen Bonding ◽  
Side Chain ◽  
Gaba Transaminase ◽  
X Ray ◽  
Potential Energy Calculations ◽  
Phenolic Oxygen ◽  
Structural Differences ◽  
Intramolecular Hydrogen

Two multisubstrate analogues of the transition state in the reaction catalysed by the enzyme GABA- transaminase (E.C. 2.6.1.19), sulfonic acid pyridoxal dervative , C10H16N2O5S (1) and carboxylic acid pyridoxal derivative, C13H18N2O4 (2), have been characterized by X-ray analyses of crystals of (1). HCl , (1).H2O and (2). HCl . In each structure, the nitrogen on the side chain is the donor in intramolecular hydrogen bonding. However, it is only in (2). HCl that this interaction is with the phenolic oxygen as postulated in the proposed transition state of the reaction catalysed by GABA- transaminase . For both structures of (1), on the other hand, this interaction is with the oxygen of the ring hydroxymethyl substituent, and results in a seven- membered ring. Conformational analysis indicates that both modes of hydrogen bonding may be present in the pyridoxal derivatives, although no quantitative assessment is possible at the MINDO/3 or MNDO levels. Simple classical potential energy calculations indicate significant structural differences between the lowest energy conformations of these compounds and the calculated transition state. However, conformations which match the key features of the transition state are also relatively low in energy.

scholarly journals Crystal structures of chlorido[dihydroxybis(1-iminoethoxy)]arsanido-κ3 N,As,N′]platinum(II) and of a polymorph of chlorido[dihydroxybis(1-iminopropoxy)arsanido-κ3 N,As,N′]platinum(II)

2020 ◽  
Vol 76 (2) ◽  
pp. 180-185
Author(s):  
Nina R. Marogoa ◽  
D.V. Kama ◽  
Hendrik G. Visser ◽  
M. Schutte-Smith
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Donor Ligands ◽  
Intermolecular Hydrogen Bonding ◽  
Π Interactions ◽  
Hydrogen Bonding Interactions ◽  
Oxygen Donor ◽  
Dimensional Network

Each central platinum(II) atom in the crystal structures of chlorido[dihydroxybis(1-iminoethoxy)arsanido-κ3 N,As,N′]platinum(II), [Pt(C4H10AsN2O4)Cl] (1), and of chlorido[dihydroxybis(1-iminopropoxy)arsanido-κ3 N,As,N′]platinum(II), [Pt(C6H14AsN2O4)Cl] (2), is coordinated by two nitrogen donor atoms, a chlorido ligand and to arsenic, which, in turn, is coordinated by two oxygen donor ligands, two hydroxyl ligands and the platinum(II) atom. The square-planar and trigonal–bipyramidal coordination environments around platinum and arsenic, respectively, are significantly distorted with the largest outliers being 173.90 (13) and 106.98 (14)° for platinum and arsenic in (1), and 173.20 (14)° and 94.20 (9)° for (2), respectively. One intramolecular and four classical intermolecular hydrogen-bonding interactions are observed in the crystal structure of (1), which give rise to an infinite three-dimensional network. A similar situation (one intramolecular and four classical intermolecular hydrogen-bonding interactions) is observed in the crystal structure of (2). Various π-interactions are present in (1) between the platinum(II) atom and the centroid of one of the five-membered rings formed by Pt, As, C, N, O with a distance of 3.7225 (7) Å, and between the centroids of five-membered (Pt, As, C, N, O) rings of neighbouring molecules with distances of 3.7456 (4) and 3.7960 (6) Å. Likewise, weak π-interactions are observed in (2) between the platinum(II) atom and the centroid of one of the five-membered rings formed by Pt, As, C, N, O with a distance of 3.8213 (2) Å, as well as between the Cl atom and the centroid of a symmetry-related five-membered ring with a distance of 3.8252 (12) Å. Differences between (2) and the reported polymorph [Miodragović et al. (2013). Angew. Chem. Int. Ed. 52, 10749–10752] are discussed.

The crystal structure of α-D-glucosamine hydrochloride and hydrobromide

1965 ◽  
Vol 285 (1403) ◽  
pp. 470-479 ◽  
Keyword(s):  
Crystal Structure ◽  
Experimental Data ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Lower Energy ◽  
Pyranose Ring ◽  
Glucosamine Hydrochloride ◽  
Ionic Hydrogen Bonding ◽  
Original Experimental Data

The crystal structures of α-D-glucosamine hydrochloride and hydrobromide have been redetermined and refined from the original experimental data. The pyranose ring of the sugar molecule has the expected normal Sachse trans configuration with the lower energy conformation 1 a 2 e 3 e 4 e 5 e . The most interesting feature of these new results is now the inter-ionic hydrogen-bonding, which is dominated by the co-ordination about the NH 3 + groups and the anions.

Crystal structures of cefdinir, C14H13N5O5S2, and cefdinir sesquihydrate C14H13N5O5S2(H2O)1.5

2019 ◽  
Vol 34 (3) ◽  
pp. 267-278
Author(s):  
Austin M. Wheatley ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
Space Group ◽  
X Ray ◽  
Additional Hydrogen

The crystal structures of cefdinir and cefdinir sesquihydrate have been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Cefdinir crystallizes in space group P21 (#4) with a = 5.35652(4), b = 19.85676(10), c = 7.57928(5) Å, β = 97.050(1) °, V = 800.061(6) Å3, and Z = 2. Cefdinir sesquihydrate crystallizes in space group C2 (#5) with a = 23.98775(20), b = 5.01646(3), c = 15.92016(12) Å, β = 109.4470(8) °, V = 1806.438(16) Å3, and Z = 4. The cefdinir molecules in the anhydrous crystal structure and sesquihydrate have very different conformations. The two conformations are similar in energy. The hydrogen bonding patterns are very different in the two structures, and the sesquihydrate is more stable than expected from the sum of the energies of cefdinir and cefdinir sesquihydrate, the result of additional hydrogen bonding. The powder patterns are included in the Powder Diffraction File™ as entries 00-066-1604 (cefdinir) and 00-066-1605 (cefdinir sesquihydrate).

Diphenyl(2-hydroxy-phenyl)phosphine and its Trimethylsilyl Ether as Ligands for Gold(I) Complexes

1999 ◽  
Vol 54 (1) ◽  
pp. 30-37 ◽  
Author(s):  
Christian Hollatz ◽  
Annette Schier ◽  
Hubert Schmidbaur
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Spectroscopic Data ◽  
Trimethylsilyl Ether ◽  
Chloro Complex

Diphenyl(2-hydroxy-phenyl)phosphine was introduced as a ligand for gold(I) halides and pentafluorophenyl gold(I) in order to probe the interplay of intra- and intermolecular interactions based on aurophilic (Au· · ·Au) and hydrogen bonding. 1:1 complexes of the type Ph2(2-HO-C6H4)P-Au-X with X = Cl, Br, C6F5 have been prepared and characterized by analytical and spectroscopic data. The crystal structure of the chloro complex (1) has been determined. In the lattice the molecules form dimers through O-H· · ·Cl hydrogen bonds. Au· · ·Au contacts are ruled out by steric congestion. Reaction of 1 with triethylamine yields a 1:1 adduct with O-H· · ·NEt3 hydrogen bonding. The trimethylsilyl ether of the title ligand also forms 1:1 complexes with AuCl, AuBr, Aul, and AuC6F5. The crystal structures of the chloro (5) and iodo (7) compound have been determined. In both cases the lattices are built from monomers which show only minor differences in their conformations. The silylether groups are not acting as intra- or intermolecular donor functions to the gold atoms.

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