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 |
|---|---|---|---|
| 1sqt | UI3 | Urokinase-type plasminogen activator | 3.4.21.73 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1sqt | UI3 | Urokinase-type plasminogen activator | 3.4.21.73 | 1.000 | |
| 2viv | VG2 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.615 | |
| 4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.589 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.544 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.501 | |
| 1ejn | AGB | Urokinase-type plasminogen activator | 3.4.21.73 | 0.498 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.497 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.483 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.483 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.482 | |
| 3v0x | ANH | Cationic trypsin | 3.4.21.4 | 0.482 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.480 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.477 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.476 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.473 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.471 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.469 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.468 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.468 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.467 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.466 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.465 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.463 | |
| 3pi5 | 3P5 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.461 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.461 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.461 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.461 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.458 | |
| 1zsk | 421 | Coagulation factor XI | 3.4.21.27 | 0.457 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.456 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.456 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.455 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.454 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.454 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.453 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.451 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.451 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.450 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.450 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.450 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.450 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.449 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.448 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.447 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.445 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.445 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.444 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.443 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.443 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.441 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.441 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1i6k | TYM | Tryptophan--tRNA ligase | 6.1.1.2 | 0.440 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.440 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.440 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.440 |