Table 1.
List of proteins analyzed, arranged by gene name. For analysis in the text, the quadrants of the pseudorotational cycle are approximately defined as (P value, ˚): (N), −45° < P ≤ 45°; (S), 135° < P ≤ 225°; (E), 45° < P ≤ 135°; (W), 225° < P ≤ 315°.
| Gene name | Protein name | representative PDB IDa | ligandb | P (˚) | ν (˚) |
|---|---|---|---|---|---|
| Purinergic Receptors | |||||
| ADORA1 | adenosine receptor A1 | 6D9H (h) | ADN | 33° | 35° |
| ADORA2A | adenosine receptor A2A | 2YDO (h) | ADN | 15° | 30° |
| ADORA2B | adenosine receptor A2B | c | |||
| ADORA3 | adenosine receptor A3 | c | |||
| P2RY1 | P2Y purinoceptor 1 | 4XNW (h) | 2ID | 340° | 25° |
| P2RY2 | P2Y purinoceptor 2 | c | |||
| P2RY4 | P2Y purinoceptor 4 | c | |||
| P2RY6 | P2Y purinoceptor 6 | c | |||
| P2RY11 | P2Y purinoceptor 11 | c | |||
| P2RY12 | P2Y purinoceptor 12 | 4PXZ (h) | 6AD | 182° | 32° |
| P2RY13 | P2Y purinoceptor 13 | c | |||
| P2RY14 | P2Y purinoceptor 14 | c | |||
| P2RX1 | P2X purinoceptor 1 | c | |||
| P2RX2 | P2X purinoceptor 2 | c | |||
| P2RX3 | P2X purinoceptor 3 | 5SVK (h) | ATP | 159° | 33° |
| P2RX4 | P2X purinoceptor 4 | 4DW1 (z) | ATP | 160° | 32° |
| P2RX5 | P2X purinoceptor 5 | c | |||
| P2RX6 | P2X purinoceptor 6 | c | |||
| P2RX7 | P2X purinoceptor 7 | 5U2H (p), 5XW6 (c) | ATP, 128 | 94°, 53° | 11°, 45° |
| Phosphatases, Cyclases, Kinases and other Enzymes | |||||
| ACPP | prostatic acid phosphatase (PAP) | ||||
| ADA1 | adenosine deaminase | 3IAR (h) | 3D1 | 40° | 39° |
| ADA2 | adenosine deaminase 2 | c | |||
| ADA | adenosine deaminase | 3KM8 (m) | 9DI | 40° | 39° |
| Adcy1 | adenylate cyclase type 1 | c | |||
| Adcy2 | adenylate cyclase type 2 | 3C16 (r) | ATP | 86° | 40° |
| Adcy3 | adenylate cyclase type 3 | c | |||
| Adcy4 | adenylate cyclase type 4 | c | |||
| Adcy5 | adenylate cyclase type 5 | c | |||
| Adcy6 | adenylate cyclase type 6 | c | |||
| Adcy7 | adenylate cyclase type 7 | c | |||
| Adcy8 | adenylate cyclase type 8 | c | |||
| Adcy9 | adenylate cyclase type 9 | c | |||
| Adcy10 | adenylate cyclase type 10 | 4USW (h) | ATP | 108° | 22° |
| ADK | adenosine kinase | 1BX4 (h), 5KB5 (m) | ADN, ADN | 97°, 106° | 47°, 40° |
| AHCY | adenosylhomocysteinase | 4PFJ (h), 5AXA (m), 1D4F (r) | ADN, ADN, ADN | 90°, 74°, 77° | 39°, 42°, 45° |
| AK1 | adenylate kinase 1 | 2C95 (h) | B4P | 170° | 44° |
| AK2 | adenylate kinase 2 | 2C9Y (h) | B4P | 172° | 36° |
| AK3 | adenylate kinase 3 | c | |||
| AK4 | adenylate kinase 4 | 2BBW (h) | GP5 | 144° | 34° |
| AK5 | adenylate kinase 5 | 2BWJ (h) | AMP | 249° | 31° |
| AK6 | adenylate kinase 6 | 3IIJ (h) | ADP | 170° | 32° |
| AK7 | adenylate kinase 7 | c | |||
| AK8 | adenylate kinase 8 | c | |||
| AK9 | adenylate kinase 9 | c | |||
| ALPI | intestinal-type alkaline phosphatase | c | |||
| ALPL | alkaline phosphatase, tissue-nonspecific isozyme (TNAP) | c | |||
| ALPP | alkaline phosphatase, placental type | c | |||
| ALPPL2 | alkaline phosphatase, germ cell type | c | |||
| AMPD1 | AMP deaminase1 | c | |||
| AMPD2 | AMP deaminase2 | c | |||
| AMPD3 | AMP deaminase3 | c | |||
| CD38 | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 2I67 (h) | APR | 156° | 35° |
| ENPP1 | ectonucleotide pyrophosphatase/phosphodiesterase family member 1 | 4GTW (m) | AMP | 151° | 36° |
| ENPP2 | ectonucleotide pyrophosphatase/phosphodiesterase family member 2 (autotaxin) | c | |||
| ENPP3 | ectonucleotide pyrophosphatase/phosphodiesterase family member 3 | 6C02 (h), 6F2V (r) | APC, AMP | 93°, 36° | 34°, 36° |
| ENPP4 | ectonucleotide pyrophosphatase/phosphodiesterase family member 4 | 4LQY (h) | AMP | 36° | 39° |
| ENTPD1 | ectonucleoside triphosphate diphosphohydrolase 1 | c | |||
| ENTPD2 | ectonucleoside triphosphate diphosphohydrolase 2 | 3CJ7 (r) | AMP | 158° | 40° |
| ENTPD3 | ectonucleoside triphosphate diphosphohydrolase 3 | c | |||
| ENTPD4 | ectonucleoside triphosphate diphosphohydrolase 4 | c | |||
| ENTPD5 | ectonucleoside triphosphate diphosphohydrolase 5 | c | |||
| ENTPD6 | ectonucleoside triphosphate diphosphohydrolase 6 | c | |||
| ENTPD7 | ectonucleoside triphosphate diphosphohydrolase 7 | c | |||
| ENTPD8 | ectonucleoside triphosphate diphosphohydrolase 8 | c | |||
| NME1 | nucleoside diphosphate kinase A | 1UCN (h) | ADP | 20° | 39° |
| NME2 | nucleoside diphosphate kinase B | 3BBF (h) | GDP | 20° | 41° |
| NME3 | nucleoside diphosphate kinase 3 | 1ZS6 (h) | ADP | 28° | 30° |
| NME4 | nucleoside diphosphate kinase, mitochondrial | c | |||
| NME6 | nucleoside diphosphate kinase 6 | c | |||
| NME7 | nucleoside diphosphate kinase 7 | c | |||
| NT5E | 5′-nucleotidase (CD73) | 4H2G (h) | ADN | 30° | 36° |
| PDE1A | Calcium/calmodulin-dependent 3′,5′-cyclic nucleotide phosphodiesterase 1A | c | |||
| PDE1B | Calcium/calmodulin-dependent 3′,5′-cyclic nucleotide phosphodiesterase 1B | c | |||
| PDE1C | Calcium/calmodulin-dependent 3′,5′-cyclic nucleotide phosphodiesterase 1C | c | |||
| PDE2A | cGMP-dependent 3′,5′-cyclic phosphodiesterase | c | |||
| PDE3A | cGMP-inhibited 3′,5′-cyclic phosphodiesterase A | c | |||
| PDE3B | cGMP-inhibited 3′,5′-cyclic phosphodiesterase B | c | |||
| PDE4A | cAMP-specific 3′,5′-cyclic phosphodiesterase 4A | c | |||
| PDE4B | cAMP-specific 3′,5′-cyclic phosphodiesterase 4B | 1ROR (h) | AMP | 49° | 37° |
| PDE4C | cAMP-specific 3′,5′-cyclic phosphodiesterase 4C | c | |||
| PDE4D | cAMP-specific 3′,5′-cyclic phosphodiesterase 4D | 2PW3 (h) | CMP | 24° | 44° |
| PDE7A | High affinity cAMP-specific 3′,5′-cyclic phosphodiesterase 7A | c | |||
| PDE7B | cAMP-specific 3′,5′-cyclic phosphodiesterase 7B | c | |||
| PDE8A | High affinity cAMP-specific and IBMX-insensitive 3′,5′-cyclic phosphodiesterase 8A | c | |||
| PDE8B | High affinity cAMP-specific and IBMX-insensitive 3′,5′-cyclic phosphodiesterase 8B | c | |||
| PDE10A | cAMP and cAMP-inhibited cGMP 3′,5′-cyclic phosphodiesterase 10A | 2OUY (h) | CMP | 27° | 42° |
| PDE11A | Dual 3′,5′-cyclic-AMP and -GMP phosphodiesterase 11A | c | |||
| PNP | purine nucleoside phosphorylase | 1RCT (h) | NOS | 56° | 16° |
| PRKAR1A | cAMP-dependent protein kinase type I-alpha regulatory subunit | 5KJX (h) | CMP | 42° | 47° |
| PRKAR2A | cAMP-dependent protein kinase type II-alpha regulatory subunit | c | |||
| PRKAR1B | cAMP-dependent protein kinase type I-beta regulatory subunit | c | |||
| PRKAR2B | cAMP-dependent protein kinase type II-beta regulatory subunit | 1CX4 (r) | CMP | 34° | 45° |
| RAPGEF1 | Rap guanine nucleotide exchange factor1 | c | |||
| RAPGEF2 | Rap guanine nucleotide exchange factor2 | c | |||
| RAPGEF3 | Rap guanine nucleotide exchange factor3 (EPAC1) | c | |||
| RAPGEF4 | Rap guanine nucleotide exchange factor4 (EPAC2) | 4MGK (m) | CMP | 43° | 40° |
| RAPGEF5 | Rap guanine nucleotide exchange factor5 | c | |||
| RAPGEF6 | Rap guanine nucleotide exchange factor6 | c | |||
| Transporters | |||||
| SLC17A9 | solute carrier family 28 member 9 (VNUT) | c | |||
| SLC28A1 | sodium/nucleoside cotransporter (CNT1) | c | |||
| SLC28A2 | sodium/nucleoside cotransporter (CNT2) | c | |||
| SLC28A3 | solute carrier family 28 member (CNT3) | c | |||
| SLC29A1 | equilibrative nucleoside transporter (ENT1) | c | |||
| SLC29A2 | equilibrative nucleoside transporter (ENT2) | c | |||
| SLC29A3 | equilibrative nucleoside transporter (ENT3) | c | |||
a.
Nucleoside/nucleotide-containing structures. The natural ligand (agonist, antagonist, substrate or product) of the protein, if present, was chosen as representative structure. Otherwise the structure at higher resolution was picked. The species is indicated in parenthesis: human (h), mouse (m), rat (r), zebrafish (z), giant panda (p), chicken (c)
b.
If more than one ligand is present in the structure, the one belonging to the first chain is indicated.
c.
Structure is not reported.