Table 1.
Fragment and ligand bound structures, fragment IDs and molecular weights in the Acpharis benchmark set, and the strongest hot spots at the fragment binding sites in both bound and unbound structures.
| No. | UniProt ID | Frag. ID | Frag. PDB IDa | Frag. MW | No. Lig.b | Max lig. PDB IDc | Max. MWd | Max RMSDe | Unbound PDB IDf | Strongest Hot Spotg | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Bound | Unbound | ||||||||||
| 1 | P55201 | 12Q | 5T4U_A | 159.19 | 1 | 5T4V | 383.42 | 0.47 | 4LC2_A | 00(19) | 00(22) |
| 2 | Q92831 | 12Q | 5FE1_A | 159.19 | 1 | 5FE9 | 266.32 | 0.27 | 5FE6_B | 00(21) | 00(24) |
| 3 | P11142 | 1LQ | 5AQP_E | 145.16 | 3 | 5AQV | 381.43 | 0.52 | 5AQM_A | 04(10) | None |
| 4 | P00918 | 1SA | 2HNC_A | 180.21 | 4 | 3MHC | 342.44 | 0.75 | 3KS3_A | 00(25) | 00(16) |
| 5 | P07900 | 2AE | 2YE6_A | 136.15 | 8 | 4AWO | 503.64 | 0.43 | 5J80_A | 01(14) | 00(22) |
| 6 | P56817 | 2AQ | 2OHL_A | 144.17 | 4 | 3RVI | 443.62 | 0.67 | 3TPJ_A | 00(16) | 01(20) |
| 7 | O60885 | 3PF | 4DON_A | 162.19 | 5 | 4E96 | 347.39 | 1.50 | 4LYI_A | 00(26) | 00(27) |
| 8 | P07900 | 42C | 3HZ1_A | 163.18 | 1 | 3HZ5 | 351.41 | 0.32 | 5J80_A | 00(22) | 00(22) |
| 9 | Q13526 | 4BX | 3KAC_A | 190.2 | 1 | 3KAH | 389.41 | 0.91 | 2ZQT_A | 00(20) | 00(17) |
| 10 | P08709 | 7XM | 5PAW_B | 159.19 | 16 | 5TQG | 681.72 | 0.58 | 1JBU_H | 00(20) | None |
| 11 | P56817 | 8AP | 2OHM_A | 199.25 | 2 | 2OHU | 421.49 | 2.26 | 3TPJ_A | 00(29) | 00(21) |
| 12 | O95696 | 8T1 | 5POE_A | 174.2 | 1 | 5POC | 283.08 | 0.54 | 5PQI_B | 03(10) | 00(24) |
| 13 | P25440 | A9P | 4ALH_A | 173.21 | 3 | 4ALG | 415.44 | 0.52 | 5IBN_A | 00(29) | 00(27) |
| 14 | B9MKT4 | ADA | 4YZ0_B | 194.14 | 1 | 4EW9 | 352.25 | 0.36 | 3T9G_A | None | None |
| 15 | P00720 | ALE | 4LDO_A | 183.2 | 2 | 4QKX | 379.47 | 0.66 | 5NDD_A | 04(09) | None |
| 16 | Q7N561 | AMG | 5ODU_C | 194.18 | 2 | 5OFI | 614.62 | 0.21 | 5OFZ_B | 01(15) | 03(13) |
| 17 | P28720 | AQO | 1S39_A | 161.16 | 43 | 4FR1 | 545.68 | 0.80 | 4Q8M A | 08(02) | 00(22) |
| 18 | P08709 | AX7 | 5PAR_C | 133.15 | 4 | 5PAI | 501.5 | 1.10 | 1JBU_H | 00(28) | None |
| 19 | P00734 | BEN | 3P70_H | 120.15 | 6 | 4BAK | 470.61 | 0.43 | 2UUF_B | 01(16) | 00(22) |
| 20 | P9WIL5 | BZ3 | 3IMC_A | 147.17 | 2 | 3IUB | 345.37 | 0.43 | 3COV_B | 01(19) | 00(26) |
| 21 | P28482 | CAQ | 4ZXT_A | 110.11 | 1 | 3SA0 | 260.2 | 0.77 | 4S31_A | 00(21) | 02(13) |
| 22 | P47228 | CAQ | 1KND_A | 110.11 | 3 | 1LKD | 255.1 | 0.25 | 1HAN_A | 00(31) | 01(15) |
| 23 | P80188 | CAQ | 3FW4_C | 110.11 | 11 | 5KID | 746.76 | 0.94 | None | 00(22) | --- |
| 24 | Q3JRA0 | CYT | 3MBM_A | 111.1 | 4 | 3K2X | 353.11 | 0.27 | None | 10(03) | --- |
| 25 | Q63T71 | CYT | 3IKE_B | 111.1 | 2 | 3IEW | 483.16 | 0.48 | None | 03(12) | --- |
| 26 | P15555 | DAL | 1IKI_A | 89.09 | 1 | 1PW1 | 429.47 | 1.61 | None | 00(22) | --- |
| 27 | P56817 | EV0 | 3HVG_A | 153.18 | 1 | 3VV8 | 331.41 | 1.96 | 3TPJ_A | 00(24) | 00(21) |
| 28 | P00918 | EVJ | 4N0X_B | 163.22 | 3 | 1I8Z | 471.57 | 0.34 | 3KS3_A | 00(26) | 00(16) |
| 29 | P00918 | FB2 | 2WEJ_A | 157.19 | 43 | 3M96 | 460.75 | 0.90 | 3KS3_A | 00(23) | 00(16) |
| 30 | P68400 | GAB | 5CSV_A | 137.14 | 2 | 5MO8 | 479.95 | 0.56 | 5CVG_A | 01(19) | 07(04) |
| 31 | P54818 | GAL | 4CCE_A | 180.16 | 1 | 4CCC | 301.25 | 0.24 | None | 00(24) | --- |
| 32 | A0A083Z | GLA | 6EQ0_B | 180.16 | 4 | 6EQ1 | 666.58 | 0.22 | None | 00(21) | --- |
| 33 | P32890 | GLA | 1DJR_G | 180.16 | 5 | 1PZI | 556.56 | 0.24 | 1LTS D | 01(18) | 02(15) |
| 34 | P42592 | GLA | 3W7U_B | 180.16 | 1 | 3W7X | 342.3 | 0.73 | 3D3I_B | 00(18) | 01(17) |
| 35 | Q57193 | GLA | 5ELB_D | 180.16 | 4 | 1PZK | 621.75 | 0.24 | 5LZJ_B | 04(11) | 03(14) |
| 36 | Q9ALJ4 | GLA | 4FNU_B | 180.16 | 1 | 4FNT | 504.44 | 0.49 | 4FNQ_A | 00(17) | 01(13) |
| 37 | P39900 | HAE | 1OS2_D | 75.07 | 5 | 1JIZ | 393.46 | 1.77 | 2MLR_A | 00(17) | None |
| 38 | Q9H2K2 | JPZ | 4PNN_B | 146.15 | 36 | 5FPG | 477.51 | 0.26 | 4PNT_D | 01(16) | None |
| 39 | P24941 | LZ1 | 2VTA_A | 118.14 | 8 | 2R64 | 453.56 | 1.28 | 4EK3_A | 00(22) | 00(29) |
| 40 | P24941 | LZ5 | 2VTL_A | 187.2 | 3 | 2VTP | 360.29 | 0.55 | 4EK3_A | 00(25) | 00(29) |
| 41 | P24941 | LZM | 2VTM_A | 144.13 | 1 | 2VTS | 313.4 | 0.92 | 4EK3_A | 00(17) | 00(29) |
| 42 | P00918 | M3T | 4Q9Y_A | 124.2 | 6 | 3M96 | 460.75 | 1.86 | 3KS3_A | 02(15) | 00(16) |
| 43 | P39900 | M4S | 3LKA_A | 187.22 | 4 | 1JIZ | 393.46 | 0.79 | 2MLR_A | 00(17) | 03(09) |
| 44 | P09874 | MEW | 4GV7_B | 160.17 | 1 | 1UK0 | 377.45 | 0.32 | 4XHU_A | 05(09) | 02(13) |
| 45 | P29477 | MR1 | 2ORQ_A | 151.16 | 2 | 1DD7 | 479.49 | 1.74 | None | None | --- |
| 46 | P29477 | MSR | 2ORQ_A | 160.17 | 3 | 2ORS | 388.38 | 0.30 | None | 01(16) | --- |
| 47 | Q10588 | NCA | 1ISM_A | 122.12 | 1 | 1ISJ | 335.23 | 0.91 | 1ISF_B | 00(25) | 00(19) |
| 48 | Q05603 | NIO | 1L4N_A | 123.11 | 1 | 1L4L | 335.2 | 0.12 | None | 04(08) | --- |
| 49 | Q08638 | NOJ | 1OIM_A | 163.17 | 1 | 2WBG | 316.39 | 0.49 | 5OSS_A | 02(18) | 01(17) |
| 50 | Q4D3W2 | ORO | 2E6A_B | 156.1 | 6 | 3W2U | 396.24 | 0.49 | None | 01(16) | --- |
| 51 | P0ABQ4 | Q24 | 3QYO_A | 160.18 | 1 | 3KFY | 302.78 | 1.03 | 1RA9_A | 00(19) | 00(32) |
| 52 | P00918 | RCO | 4E49_A | 110.11 | 2 | 4FIK | 282.33 | 0.32 | 5DSR_A | 02(16) | None |
| 53 | P19491 | SHI | 1MS7_A | 172.14 | 2 | 1N0T | 322.25 | 0.53 | None | 04(11) | --- |
| 54 | P06820 | ST3 | 1IVE_A | 194.19 | 2 | 1INH | 252.25 | 0.96 | 4H53_D | 00(29) | None |
| 55 | Q6PL18 | TDR | 4QSU_A | 126.11 | 3 | 4QSW | 258.23 | 0.33 | 4QSQ_A | 01(21) | 00(23) |
| 56 | Q6TFC6 | TDR | 3FS8_B | 126.11 | 2 | 3FSB | 547.35 | 0.48 | None | None | --- |
| 57 | Q8K4Z3 | TDR | 3RO7_A | 126.11 | 2 | 3ROG | 322.21 | 0.85 | None | 00(22) | --- |
| 58 | P25440 | TVP | 4A9H_A | 189.25 | 1 | 4UYF | 434.92 | 0.19 | 5IBN_A | 00(24) | 00(27) |
| 59 | Q92793 | TYL | 4A9K_B | 151.16 | 1 | 5I83 | 296.36 | 2.16 | 5KTU_B | 00(26) | 00(25) |
| 60 | P07900 | XQ0 | 2YEC_A | 148.16 | 7 | 5ODX | 493.56 | 0.59 | 5J80_A | 00(28) | 00(22) |
| 61 | Q9WYE2 | ZWZ | 2ZWZ_A | 176.21 | 5 | 2ZX5 | 347.41 | 0.31 | 1HL8_B | 02(13) | 00(28) |
| 62 | P16083 | ZXZ | 3NHW_A | 173.21 | 2 | 3NHK | 263.29 | 0.94 | None | None | --- |
a
PDB ID and chain ID of the structure with bound fragment
b
Number of ligands binding to the protein and containing the fragment as substructure
c
PDB ID of the protein in complex with the largest ligand
d
Molecular weight of the largest ligand
e
Maximum RMSD between the fragment and the corresponding atoms as substructure in any of the ligands
f
PDB ID and chain ID of the unbound structure. “None” indicates that no unbound structure is available in the PDB.
g
Strongest hot spot with at least 50% coverage of the fragment binding site. Hot spots are numbered starting at 00 as established in the FTMap server. The number of probe clusters in given in parenthesis. “None” indicates that no such hot spot is found. ”---” shows that there is no unbound structure.