sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3egk | M18 | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3egk | M18 | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.749 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.741 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.691 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.662 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.659 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.659 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.647 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.643 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.640 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.638 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.637 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.632 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.624 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.616 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.612 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.611 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.610 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.610 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.602 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.601 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.598 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.598 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.593 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.593 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.590 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.590 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.587 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.587 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.587 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.586 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.583 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.575 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.569 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.568 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.568 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.563 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.563 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.562 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.560 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.559 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.557 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.554 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.553 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.552 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.551 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.550 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.548 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.547 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.547 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.540 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.538 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.537 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.535 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.534 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.530 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.529 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.529 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.529 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.527 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.524 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.520 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.518 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.515 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.513 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.513 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.512 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.507 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.505 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.504 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.499 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.498 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.495 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.494 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.493 | |
| 2g00 | 4QC | Coagulation factor X | 3.4.21.6 | 0.484 | |
| 4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.482 | |
| 2viv | VG2 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.481 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.473 | |
| 1zsk | 421 | Coagulation factor XI | 3.4.21.27 | 0.472 | |
| 3v2u | ATP | Protein GAL3 | / | 0.471 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.465 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.464 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.463 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3v0x | ANH | Cationic trypsin | 3.4.21.4 | 0.460 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.455 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.455 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.455 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.455 | |
| 1sqt | UI3 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.454 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.451 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.449 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.448 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3juq | AKD | Phenazine biosynthesis protein A/B | / | 0.447 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.442 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2ft0 | ACO | dTDP-fucosamine acetyltransferase | / | 0.441 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.441 | |
| 1zdw | FLV | Prenyltransferase | / | 0.440 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.440 |