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NUDT7

In the deposition group G_1002045 are the following molecules:

pdb_id type pdb_filename ligand_resn chembl_id formal_charge SMILES systematic_name title_name paper_name
5QGG hit 5qgg.pdb H2G 0 CC@HCNCc1sc(C)cc1 (2S)-1-{[(5-methylthiophen-2-yl)methyl]amino}propan-2-ol FMOPL000693a nan
5QGH hit 5qgh.pdb H2D 0 CCC@@Hc2ccccc2 (2R)-N-(1,2-oxazol-3-yl)-2-phenylbutanamide FMOPL000420a nan
5QGI hit 5qgi.pdb B0V 0 COCC(=O)Nc1c(C)cc(C)cc1C 2-methoxy-~{N}-(2,4,6-trimethylphenyl)ethanamide FMOPL000710a nan
5QGJ hit 5qgj.pdb H1A 0 CCC(CC)C(=O)Nc1ccccc1O 2-ethyl-N-(2-hydroxyphenyl)butanamide FMOPL000706a nan
5QGK hit 5qgk.pdb H0S 0 Cc1ccc(Nc2ncnc3[nH]ncc23)cc1 N-(4-methylphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine FMOPL000679a nan
5QGL hit 5qgl.pdb H5A 0 COc1cc(cc(OC)c1OC)C(O)=O 3,4,5-trimethoxybenzoic acid FMOPL000275a nan
5QGM hit 5qgm.pdb H4Y 0 COc1ccc(cc1)c2ccccc2N3CCCC3=O 1-(4'-methoxy[1,1'-biphenyl]-2-yl)pyrrolidin-2-one OX-160 Compound 3A
5QGN hit 5qgn.pdb H4D 0 OB(O)c1cc(NC(=O)Cc2sccc2)cc(c1)C(O)=O 3-borono-5-{[(thiophen-2-yl)acetyl]amino}benzoic acid OX-210 nan
5QGO hit 5qgo.pdb H4A 0 O[C@@H]1CC@@Hc4ccccc4 (3aR,4R,6R,7R,8aR)-6-phenyloctahydro-1H-3a,7-epiminocyclohepta[c]pyrrol-4-ol OX-220 nan
5QGP hit 5qgp.pdb H3Y 0 O[C@H]1CC@@Hc4ccccc4 (3aR,4S,6R,7R,8aR)-6-phenyloctahydro-1H-3a,7-epiminocyclohepta[c]pyrrol-4-ol OX-221 nan
5QGQ hit 5qgq.pdb H3J 0 CC1=C(Oc2cccnc2)C(=O)C=C1 3-methyl-2-[(pyridin-3-yl)oxy]cyclopenta-2,4-dien-1-one OX-65 nan
5QGR hit 5qgr.pdb H0J 0 NC(=S)c1sc(cc1)c2ccccn2 5-(pyridin-2-yl)thiophene-2-carbothioamide FMOPL000022a nan
5QGS hit 5qgs.pdb H0D 0 CCC@HNC(=O)Nc1ccc(Cl)cc1 N-(4-chlorophenyl)-N'-[(2R)-1-hydroxybutan-2-yl]urea FMOPL000476a nan
5QGT hit 5qgt.pdb H04 0 CCOc1ccccc1N2CCNCC2 1-(2-ethoxyphenyl)piperazine FMOPL000609a nan
5QGU hit 5qgu.pdb H3G 0 CC(C)(C)C1CCN(CC1)C(=O)c2ccccc2 (4-tert-butylpiperidin-1-yl)(phenyl)methanone FMOPL000747a nan
5QGV hit 5qgv.pdb H3A 0 COc1cccc(CC(=O)Nc2cccc(Cl)c2)c1 N-(3-chlorophenyl)-2-(3-methoxyphenyl)acetamide UNUYB062989 nan
5QGW hit 5qgw.pdb H2Y 0 COc1ccc(CC(=O)Nc2cccnc2)cc1 2-(4-methoxyphenyl)-N-(pyridin-3-yl)acetamide NUOOA000154 nan
5QGX hit 5qgx.pdb H2J 0 COc1ccc(CC(=O)Nc2cccc(Cl)c2)cc1 N-(3-chlorophenyl)-2-(4-methoxyphenyl)acetamide NUOOA000155 nan
5QGY hit 5qgy.pdb H1Y 0 Clc1cccc(NC(=O)Cc2ccccc2)c1 N-(3-chlorophenyl)-2-phenylacetamide NUOOA000158 nan
5QGZ hit 5qgz.pdb H1J 0 Fc1ccc(CC(=O)Nc2cccc(Cl)c2)cc1 N-(3-chlorophenyl)-2-(4-fluorophenyl)acetamide NUOOA000161 nan
5QH0 hit 5qh0.pdb H0P 0 Oc1cccc(CC(=O)Nc2cccnc2)c1 2-(3-hydroxyphenyl)-N-(pyridin-3-yl)acetamide NUOOA000180 nan
5QH1 hit 5qh1.pdb H5G 0 Oc1cccc(CC(=O)Nc2cccc(Cl)c2)c1 N-(3-chlorophenyl)-2-(3-hydroxyphenyl)acetamide NUOOA000181 NU181
5QH2 hit 5qh2.pdb H54 0 Cc1cccc(CC(=O)Nc2cccnc2)c1 2-(3-methylphenyl)-N-(pyridin-3-yl)acetamide NUOOA000188 nan
5QH3 hit 5qh3.pdb H4G 0 Fc1ccc(CC(=O)Nc2cccnc2)c(F)c1 2-(2,4-difluorophenyl)-N-(pyridin-3-yl)acetamide NUOOA000191 nan
5QH4 hit 5qh4.pdb H47 0 COc1cccc(CC(=O)Nc2ccon2)c1 2-(3-methoxyphenyl)-N-(1,2-oxazol-3-yl)acetamide NUOOA000220a nan
5QH5 hit 5qh5.pdb H3V 0 O=C(Cc1ccccc1)Nc2ccon2 N-(1,2-oxazol-3-yl)-2-phenylacetamide NUOOA000224a nan
5QH6 hit 5qh6.pdb H0M 0 Oc1cccc(CC(=O)Nc2ccccn2)c1 2-(3-hydroxyphenyl)-N-(pyridin-2-yl)acetamide NUOOA000259a nan
5QH7 hit 5qh7.pdb H0G 0 Cc1cccc(CC(=O)Nc2ccon2)c1 2-(3-methylphenyl)-N-(1,2-oxazol-3-yl)acetamide NUOOA000194a nan
5QH8 hit 5qh8.pdb H0A 0 COc1ccc(cc1)[C@@H]2CC=CCCN2C(C*)=O 1-[(2S)-2-(4-methoxyphenyl)-2,3,6,7-tetrahydro-1H-azepin-1-yl]ethan-1-one PCM-0102558 nan
5QH9 hit 5qh9.pdb GZY 0 COc1cccc(c1)[C@@H]2CCCN2C(C*)=O 1-[(2S)-2-(3-methoxyphenyl)pyrrolidin-1-yl]ethan-1-one PCM-0102716 nan
5QHA hit 5qha.pdb H3D 0 *CC(=O)NC1(CCCC1)c2ccc3OCCOc3c2 N-[1-(2,3-dihydro-1,4-benzodioxin-6-yl)cyclopentyl]acetamide PCM-0102951 nan
5QHB hit 5qhb.pdb H31 0 Cc1ccc(cc1)c2ccccc2N3CCCC3=O 1-(4'-methyl[1,1'-biphenyl]-2-yl)pyrrolidin-2-one RK4-332 Compound 3D
5QHC hit 5qhc.pdb H2M 0 FC(F)(F)c1cccc(c1)c2ccccc2N3C=CCC3=O 1-[3'-(trifluoromethyl)[1,1'-biphenyl]-2-yl]-1,3-dihydro-2H-pyrrol-2-one RK4-337 Compound 3C
5QHE hit 5qhe.pdb H1P 0 Fc1ccc(cc1)c2ccccc2N3C=CCC3=O 1-(4'-fluoro[1,1'-biphenyl]-2-yl)-1,3-dihydro-2H-pyrrol-2-one RK4-350 Compound 3F
5QHF hit 5qhf.pdb H1G 0 COc1ccc(CC(=O)Nc2cncc(OCC(=O)N3CCNC(=O)C3)c2)cc1 2-(4-methoxyphenyl)-N-{5-[2-oxo-2-(3-oxopiperazin-1-yl)ethoxy]pyridin-3-yl}acetamide NUOOA000301a nan
5QHG hit 5qhg.pdb H17 0 Clc1cccc(NC(=O)Cc2cccc(c2)[C@H]3CCCN3C(=O)C=C)c1 2-{3-[(2R)-1-acryloylpyrrolidin-2-yl]phenyl}-N-(3-chlorophenyl)acetamide NU000442a nan
5QHH hit 5qhh.pdb H5D 0 *CC(=O)N1CCC[C@H]1c2cccc(CC(=O)Nc3cccc(Cl)c3)c2 2-{3-[(2S)-1-acetylpyrrolidin-2-yl]phenyl}-N-(3-chlorophenyl)acetamide NU000443a NU443

The JACS paper calls NUOOA000181 NUDT7-REV-1, while the ChemMedChem paper calls it NU181. This was merged with PCM-0102716 to make NUDT7-COV-1.

But there appear to be two chiralities: NU000443a is S and NU000442a is R. The latter, were it reacted would be '*CC(=O)N1CCC[C@@H]1c1cccc(CC(=O)Nc2cccc(Cl)c2)c1'.

The latter scores 1.1 kcal/mol higher (–9.2 kcal/mol) than the former (–10.3 kcal/mol) and the SG atom in NU443 is only .3 Å away from where it is in PCM-0102716, while in NU442 it is .9 Å away. but this is far from a smoking gun to explain why it did not react. To do that one would need to model the reaction-readied state of the molecule, which takes time to set up correctly.