Sodium in PDB, part 244 (files: 9721-9760),
PDB 7g49-7g5t
Experimental structures of coordination spheres of Sodium (Na) in bioorganic
molecules from X-Ray and NMR experiments. Coordination spheres were calculated with 5.0 Angstroms radius
around Sodium atoms. PDB files: 9721-9760 (PDB 7g49-7g5t).
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7g49 (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One
Other atoms:
Ca (1);
Cl (1);
Zn (1);
F (1);
-
7g4b (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4- (Trifluoromethyl)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H- Benzotriazole-5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 Microm
Other atoms:
F (8);
K (1);
Zn (1);
Cl (1);
Ca (2);
-
7g4c (Na: 3) - Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm
Other atoms:
Ca (1);
Cl (1);
Zn (1);
-
7g4h (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm
Other atoms:
Ca (2);
Cl (1);
Zn (1);
K (1);
F (6);
-
7g4k (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm
Other atoms:
Ca (1);
Cl (3);
Zn (1);
-
7g4l (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with N-[2-Amino-4-[3-[4- (Trifluoromethyl)Phenyl]Propanoyl]Phenyl]Acetamide, I.E. Smiles C1C(Ccc(C1N)Nc(=O)C)C(=O)CCC1CCC(CC1)C(F)(F)F with IC50=0.529423 Microm
Other atoms:
Ca (1);
Zn (1);
Cl (1);
F (3);
-
7g4m (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with N-Benzyl-2-(4- Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)-N-Phenylacetamide
Other atoms:
Ca (1);
Zn (1);
Cl (1);
K (1);
-
7g4n (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm
Other atoms:
Zn (1);
Cl (1);
Ca (1);
F (3);
-
7g4o (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm
Other atoms:
Ca (1);
Zn (1);
-
7g4q (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 Microm
Other atoms:
Ca (1);
Zn (1);
Cl (2);
-
7g4r (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm
Other atoms:
Ca (1);
Cl (4);
Zn (1);
-
7g4s (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with 3-(4-Chlorophenyl)- 5-Methyl-N-(Oxolan-2-Ylmethyl)Pyrazolo[1,5-A]Pyrimidin-7-Amine, I.E. Smiles C12=C(C=NN1C(=Cc(=N2)C)Nc[C@@H]1OCCC1)C1CCC(CC1)Cl with IC50=0.95455 Microm
Other atoms:
Ca (1);
Cl (2);
Zn (1);
-
7g4t (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with (6-Bromonaphthalen- 2-Yl)-[Rac-(1R,2R,6S,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CCC2C(C1)Ccc(C2)Br with IC50=0.127386 Microm
Other atoms:
Ca (1);
Zn (1);
Cl (1);
Br (1);
-
7g4u (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm
Other atoms:
F (3);
Zn (1);
Ca (1);
-
7g4w (Na: 3) - Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm
Other atoms:
Cl (2);
Zn (1);
K (1);
Ca (1);
-
7g4x (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with N'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 Microm
Other atoms:
Ca (1);
K (1);
Cl (1);
Zn (1);
-
7g4y (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm
Other atoms:
F (3);
Ca (2);
Cl (1);
Zn (1);
K (1);
-
7g4z (Na: 2) - Crystal Structure of Rat Apo Autotaxin
Other atoms:
Ca (2);
Cl (1);
-
7g51 (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with (5Z)-5-[(4- Phenoxyphenyl)Methylidene]-2-Pyrrolidin-1-Yl-1,3-Thiazol-4-One, I.E. Smiles C\1(=C\C2CCC(OC3CCCCC3)CC2)/C(=O)N=C(S1)N1CCCC1 with IC50=0.135695 Microm
Other atoms:
Ca (1);
Cl (1);
Zn (1);
K (1);
-
7g52 (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 Microm
Other atoms:
Ca (2);
Zn (1);
Cl (1);
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7g53 (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-(2-Methoxyethoxy)Quinoline-2-Carbonyl]-4, 9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1NC2C(C(C1)Occoc)CCCC2 with IC50=0.223388 Microm
Other atoms:
K (1);
Cl (1);
Zn (1);
Ca (1);
-
7g55 (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm
Other atoms:
Zn (1);
Cl (1);
Ca (1);
F (3);
-
7g56 (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 Microm
Other atoms:
Zn (1);
Ca (1);
-
7g58 (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm
Other atoms:
Zn (1);
Cl (1);
Ca (2);
-
7g59 (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm
Other atoms:
F (16);
Ca (2);
Zn (1);
Cl (1);
-
7g5a (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with 2-Tert-Butyl-6-(4- Chlorophenyl)-4-Methylsulfonylpyridine, I.E. Smiles C1(C2CCC(CC2)Cl) Cc(Cc(N1)C(C)(C)C)S(=O)(=O)C with IC50=2.51866 Microm
Other atoms:
Zn (1);
Cl (2);
Ca (1);
-
7g5b (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 Microm
Other atoms:
Zn (1);
Ca (1);
F (1);
-
7g5c (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm
Other atoms:
Zn (1);
Cl (1);
K (1);
Ca (1);
F (6);
-
7g5d (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with [(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-[4-(4-Chlorophenyl)Phenyl]Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CCC(CC1)C1CCC(CC1)Cl)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.00428865 Microm
Other atoms:
Ca (1);
Cl (1);
Zn (1);
-
7g5e (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with Rac-(4S,6R,7S,8S, 11S,12S,15R,16R)-4,6-Dihydroxy-12,16-Dimethyl-15-[Rac-(2R)-6-Methyl- 5-Methylidene-4-Oxoheptan-2-Yl]Pentacyclo[9.7.0.01,3.03,8.012, 16]Octadecane-7-Carboxylic Acid, I.E. Smiles [C@@]123[C@@]4(C1) [C@H]([C@]1([C@](CC4)([C@H](CC1)[C@@H](Cc(=O)C(=C)C(C)C)C)C)C) Cc[C@H]2[C@@H]([C@@H](C[C@@H]3O)O)C(=O)O with IC50=0.0603796 Microm
Other atoms:
Ca (1);
Zn (1);
-
7g5f (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[4-(Cyclopropylmethoxy)Naphthalene-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 Microm
Other atoms:
Cl (1);
Zn (1);
Ca (1);
-
7g5g (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with 1-[2- (Cyclohexylmethyl)-1,3-Dioxoisoindol-4-Yl]-N-[(4-Methyl-1,2,5- Oxadiazol-3-Yl)Methyl]Piperidine-4-Carboxamide, I.E. Smiles N1(C(=O) C2C(C1=O)CCCC2N1CCC(C(=O)NCC2=Non=C2C)CC1)CC1CCCCC1 with IC50=0.0435744 Microm
Other atoms:
Ca (1);
Zn (1);
-
7g5j (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with (7E)-7-[(4- Bromophenyl)Methylidene]-12H-Isoquinolino[2,3-A]Quinazolin-5-One, I.E. Smiles N12C(=Nc(=O)C3C1CCCC3)/C(=C/C1CCC(CC1)Br)/C1C(C2)CCCC1 with IC50=0.173306 Microm
Other atoms:
K (1);
Zn (1);
Ca (1);
Br (1);
-
7g5k (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm
Other atoms:
Ca (1);
K (1);
Cl (3);
Zn (1);
-
7g5n (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm
Other atoms:
Cl (1);
Zn (1);
Ca (3);
-
7g5p (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm
Other atoms:
Cl (1);
Zn (1);
Ca (1);
F (3);
-
7g5q (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm
Other atoms:
F (3);
Zn (1);
Ca (2);
-
7g5r (Na: 2) - Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm
Other atoms:
Ca (2);
Cl (1);
Zn (1);
F (3);
-
7g5s (Na: 1) - Crystal Structure of Rat Autotaxin in Complex with (4-Cyano-2- Ethoxyphenyl)Methyl (3AS,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A, 4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)OCC1C(Cc(CC1)C#N)Occ)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.122624 Microm
Other atoms:
Ca (1);
K (1);
Zn (1);
Cl (1);
-
7g5t (Na: 3) - Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm
Other atoms:
F (4);
Zn (1);
Cl (1);
Ca (2);
Page generated: Tue Feb 25 11:40:30 2025
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