Table 1.
Test Set Composition.
| Complex PDB ID (chain ID) | Protein name | No. of residues | CATH ID | Ligand ID | Template PDB ID | Seq_Id (%) |
|---|---|---|---|---|---|---|
| 1A28 (A) | Progesterone receptor | 256 | 1.10.565.10 | STR | 1NQ7 1YUC 2AM9 |
17 21 55 |
| 1A4Q(A) | Neuraminidase | 390 | 2.120.10.10 | DPC | 1V0Z 2BAT 2HT5 2HTV |
31 32 35 37 |
| 1ABF | L-arabinose binding protein | 306 | 3.40.50.2300 | FCA | 1TLF 2DRI 2GBP |
18 21 22 |
| 1C83 (A) | Protein-tyrosine Phosphatase 1B | 298 | 3.90.190.10 | OAI | 1RPM 2GJT |
34 37 |
| 1CBS | Cellular retinoic-acid-binding protein type II | 137 | 2.40.128.20 | REA | 1MDC 2FT9 3IFB 1FTP 1CBI |
24 27 30 38 77 |
| 1EJN (A) | Urokinase-type plasminogen activator | 253 | 2.40.10.10 | AGB | 1OP8 1PPF 1ELT 1YBW |
23 26 33 38 |
| 1ETA (1) | Transthyretin (prealbumin) | 127 | 2.60.40.180 | T44 | 1OO2 1TFP 1IE4 |
56 79 84 |
| 1FEN | Retinol binding protein | 183 | 2.40.128.20 | AZE | 1EXS 1IIU |
21 82 |
| 1LST | Lysine-, arginine-, ornithine-binding protein | 239 | 3.40.109.10 | LYS | 1XT8 1GGG 1HSL |
25 30 71 |
| 1MLD (A) | Malate dehydrogenase | 314 | 3.40.50.720 | CIT | 1I0Z 2LDX 6LDH 1HYG 1SMK 1EMD |
19 23 24 27 56 59 |
| 1MRG | α-Momorcharin | 263 | 3.40.420.10 | ADN | 1QI7 1WUC 1ABR 1HWM 1CF5 1MRJ 1BRY 1NIO |
24 29 33 36 53 64 66 70 |
| 1MRK | α-Trichosanthin | 247 | 3.40.420.10 | FMC | 1R4P 1RL0 1APA 2MLL 1RTC 1NIO 1CF5 1MRG |
17 22 29 33 37 60 62 64 |
| 1ROB | Ribonuclease A | 124 | 3.10.130.10 | C2P | 1OJ1 1DYT 1ONC 1B1I 1AGI 1RNF 1Z7X |
27 28 30 32 36 42 70 |
| 1SRJ (A) | Streptavidin | 121 | 2.40.128.30 | NAB | 1WBI 1Y52 |
27 30 |
| 1TNG | Trypsin | 229 | 2.40.10.10 | AMC | 1QY6 1A7S 1FIW 1YBW 2F91 1HJ8 1H4W 1A0J 1TRN 2A31 |
15 30 34 38 43 66 73 74 75 82 |
| 1UKZ | Uridylate kinase | 203 | 3.40.50.300 | AMP | 1G3U 1GKY 1AKE 1Z83 1TEV 1UKE |
17 23 28 44 48 52 |
| 2AK3 (A) | Adenylate kinase isoenzyme-3 | 226 | 3.40.50.300 | AMP | 1MV5 1VHL 1TEV 1Z83 1UKE 2AK2 2AKY 2AR7 |
18 19 25 26 27 40 41 58 |
| 3CLA | Chloramphenicol Acetyltransferase | 213 | 3.30.559.10 | CLM | 1NOC | 47 |
| 3ERT (A) | Estrogen receptor alpha | 261 | 1.10.565.10 | OHT | 1NQ7 1PK5 |
21 24 |
| 6RNT | Ribonuclease T1 | 104 | 3.10.450.30 | 2AM | 1RMS | 65 |
| 7TIM (A) | Triosephosphate isomerase | 247 | 3.20.20.70 | PGH | 1B9B 1R2R 1WYI 1MO0 |
43 53 53 54 |
The first five columns report the characteristics of the ligand-protein complexes in the reference set of X-ray structures; the last two columns refer to the templates selected for homology modeling and their sequence identities with the target.