Table 1 Examples of frequently transplanted compounds in the AlphaFill databank for indicative levels of sequence identity: trans., transplants
From: AlphaFill: enriching AlphaFold models with ligands and cofactors
Sequence identity | 25% | 30% | 50% | 70% | |||||
|---|---|---|---|---|---|---|---|---|---|
Compound code and name | No. of entries | No. of transplants | No. of entries | No. of transplants | No. of entries | No. of transplants | No. of entries | No. of transplants | |
Nucleotides | |||||||||
ADP | Adenosine diphosphate | 100,258 | 242,131 | 77,591 | 166,420 | 26,804 | 42,189 | 10,076 | 13,975 |
AMP | Adenosine monophosphate | 59,639 | 102,608 | 44,548 | 68,972 | 12,811 | 18,334 | 3,951 | 4,881 |
ATP | Adenosine triphosphate | 67,807 | 119,001 | 51,155 | 83,267 | 14,729 | 22,765 | 5,226 | 7,223 |
GDP | Guanosine diphosphate | 30,839 | 77,253 | 23,810 | 51,240 | 10,986 | 16,702 | 4,831 | 6,353 |
GTP | Guanosine triphosphate | 18,274 | 30,586 | 14,443 | 23,841 | 5,139 | 7,974 | 2,054 | 2,896 |
UDP | Uridine diphosphate | 17,717 | 25,197 | 11,119 | 14,091 | 2,787 | 3,184 | 858 | 1,040 |
Cofactors | |||||||||
COA | Coenzyme A | 19,037 | 61,080 | 12,344 | 40,880 | 3,162 | 11,751 | 1,369 | 3,109 |
FAD | Flavin adenine dinucleotide | 18,406 | 50,295 | 10,851 | 23,667 | 3,111 | 4,564 | 1,470 | 1,958 |
FMN | Flavin mononucleotide | 11,892 | 26,072 | 7,732 | 15,929 | 2,611 | 4,054 | 1,225 | 1,719 |
GSH | Glutathione | 9,764 | 20,884 | 7,535 | 14,186 | 2,113 | 3,021 | 851 | 1,122 |
HEM | Heme | 18,675 | 45,968 | 11,586 | 28,849 | 6,000 | 13,737 | 4,242 | 7,850 |
NAD | Nicotinamide adenine dinucleotide | 35,016 | 82,533 | 24,284 | 50,799 | 8,542 | 14,186 | 3,087 | 4,898 |
NAI | NADH | 17,223 | 24,848 | 11,370 | 15,858 | 2,881 | 3,858 | 796 | 1,125 |
NAP | NAD phosphate/NADP | 26,467 | 67,179 | 18,142 | 38,576 | 4,355 | 8,286 | 1,577 | 2,311 |
NDP | NADPH | 21,598 | 42,241 | 14,291 | 26,603 | 3,660 | 7,383 | 1,535 | 2,937 |
PLP | Pyridoxal phosphate | 13,462 | 158,684 | 10,119 | 94,516 | 5,016 | 12,904 | 2,131 | 4,978 |
SAH | S-Adenosyl-l-homocysteine | 21,121 | 30,189 | 15,692 | 19,778 | 4,184 | 5,079 | 1,399 | 1,629 |
SAM | S-adenosylmethionine | 21,072 | 32,467 | 16,239 | 23,465 | 4,449 | 7,361 | 1,890 | 2,948 |
Miscellaneous | |||||||||
CLA | Chlorophyll A | 3,505 | 443,127 | 3,217 | 425,290 | 1,502 | 171,022 | 1,375 | 157,851 |
CLR | Cholesterol | 8,533 | 53,500 | 4,310 | 18,184 | 532 | 1,654 | 339 | 866 |
Metal ions | |||||||||
CA | Calcium(2+) ion | 202,360 | 759,181 | 145,813 | 473,734 | 40,010 | 117,321 | 15,910 | 47,819 |
K | Potassium(1+) ion | 117,813 | 270,758 | 86,633 | 189,961 | 23,999 | 51,361 | 7,239 | 13,707 |
MG | Magnesium(2+) ion | 328,108 | 1,981,187 | 264,320 | 1,576,629 | 95,618 | 514,634 | 33,595 | 91,445 |
NA | Sodium(1+) ion | 272,353 | 1,067,005 | 204,482 | 734,824 | 57,076 | 176,645 | 19,793 | 53,329 |
ZN | Zinc(2+) ion | 186,268 | 639,282 | 135,426 | 417,736 | 41,808 | 99,486 | 16,675 | 36,315 |
